Prejudice, hatred and retaliation by God against individuals and religious groups

“God is described as exhibiting intolerance and anger towards humans in many Biblical passages:

God rejected a sincere offering:

Adam and Eve had two sons: Cain, a farmer, and Abel, a shepherd. Both gave an offering to God: The former was a vegetable sacrifice; the latter, animal. The Lord had no respect for either Cain or his offering. This triggered Cain's murder of his brother. Liberal theologians are divided on their interpretation of this passage. Some believe it originated in a story of ritual human sacrifice. Others suspect that God rejected Cain's sacrifice as inadequate because it was plant and not animal. Many religious conservatives believe that God's rejection of Cain and his sacrifice was related to unconfessed sin in his life. Hebrews 11:4 supports the latter interpretation.
Genesis 4:2-5 "...And Abel was a keeper of sheep, but Cain was a tiller of the ground... it came to pass, that Cain brought of the fruit of the ground an offering unto the LORD. And Abel, he also brought of the firstlings of his flock and of the fat thereof. And the LORD had respect unto Abel and to his offering: But unto Cain and to his offering he had not respect. And Cain was very wroth, and his countenance fell."


God killed the inhabitants of Sodom and Gomorrah:

God exterminated all of the inhabitants (men, women, children, infants, newborns) of these two towns. Although many denominations teach that the crime for which God punished these people was homosexual behavior, other verses in the Bible show that the actual crime was their lack of kindness towards and abusive of strangers. 
Genesis 19:24-25 "Then the LORD rained upon Sodom and upon Gomorrah brimstone and fire from the LORD out of heaven; And he overthrew those cities, and all the plain, and all the inhabitants of the cities, and that which grew upon the ground."


God killed Onan because he avoided his duty to impregnate his sister-in-law:

God had killed Er because he was wicked. This gave his brother, Onan, the religious obligation to engage in sexual intercourse with Er's widow. The resulting baby would be considered Er's offspring. Onan did not want to impregnate Er's wife. The exact reason is unknown. He practiced an elementary (and unreliable) form of birth control: coitus interruptus. God killed him because he did not perform his religious duty. These verses were used in the past to condemn masturbation. That appears to be based on a misinterpretation of the passage.
Genesis 38: 7-10 "And Er, Judah's firstborn, was wicked in the sight of the LORD; and the LORD slew him. And Judah said unto Onan, Go in unto thy brother's wife, and marry her, and raise up seed to thy brother. And Onan knew that the seed should not be his; and it came to pass, when he went in unto his brother's wife, that he spilled it on the ground, lest that he should give seed to his brother. And the thing which he did displeased the LORD: wherefore he slew him also."


God killed Lot's wife:

Some men, who were actually angels, told Lot and his family to flee from Sodom, advising them to not look back or stop until they reached the mountains. Lot negotiated with the men to get permission to only flee to a nearby town, Zoar instead of to the mountains. The men agreed. Once they had reached Zoar, had met of the instructions of the men, and were safe, Lot's wife seems to have assumed that they could look back at the devastation -- at Sodom which contained the remains of her son-in-laws, her more distant relatives (if any) and her friends. God killed her and changed her to a pillar of salt.
Genesis 19:26 "But his wife looked back from behind him, and she became a pillar of salt"


God attempted to kill Moses:

After God selected Moses to lead his people out of Egypt, he apparently changed his mind and attempted to kill him. His wife Zipporah took a piece of flint, amputated her son's foreskin and touched Moses' feet with it. This apparently prevented God from killing Moses. ("Feet" in ancient Hebrew were sometimes used to refer to male genitals). The story does not make a great deal of sense; theologians have debated over its meaning for centuries without resolution.
Exodus 4:24-26 "...the LORD met him, and sought to kill him. Then Zipporah took a sharp stone, and cut off the foreskin of her son, and cast it at his feet, and said, Surely a bloody husband art thou to me."


God killed untold numbers of Egyptians:

God selected Moses to lead his people out of Egypt. But God also "hardened the heart" of the Pharaoh (Exodus 4:21, 7:3, 14:4 and 14:17) so that the Pharaoh would not readily let the Jews leave. The result was a series of 10 plagues of increasing severity, culminating in the death of every first born human and animal in Egypt (except for the Jews who had sprinkled blood on their doorposts). Finally, the Pharaoh allowed the Jews to depart.
Exodus 12:29 "And it came to pass, that at midnight the LORD smote all the firstborn in the land of Egypt, from the firstborn of Pharaoh that sat on his throne unto the firstborn of the captive that was in the dungeon; and all the firstborn of cattle. And Pharaoh rose up in the night, he, and all his servants, and all the Egyptians; and there was a great cry in Egypt; for there was not a house where there was not one dead."


Religious civil war among the Israelites:

Two religions were followed by the Israelites at the time: one group worshipped Pagan Gods; the other worshipped the God of the Torah. God was displeased, and decided to break his promises to Abraham, Isaac and Israel. He was prepared to destroy all of the Israelites because of the religious beliefs of the Pagan minority. Moses convinced God to permit just the slaughter of the 3,000 adult male Pagans, and their wives and children.
Exodus 32:28 "...Put every man his sword by his side, and go in and out from gate to gate throughout the camp, and slay every man his brother, and every man his companion, and every man his neighbor. And children of Levi did according to the word of Moses: and there fell of the people that day about three thousand men."


God ordered Israelites to destroy Pagan temples:

God ordered the Israelites to drive various Pagan tribes out of Palestine, and to desecrate the religious altars, obelisks and idols that had been used in worship. God later orders that they not inter-marry with people from other tribes.
Exodus 34:11 "...behold, I drive out before thee the Amorite, and the Canaanite, and the Hittite, and the Perizzite, and the Hivite, and the Jebusite. Take heed to thyself, lest thou make a covenant with the inhabitants of the land whither thou goest, lest it be for a snare in the midst of thee: But ye shall destroy their altars, break their images, and cut down their groves: For thou shalt worship no other god: for the LORD, whose name is Jealous, is a jealous God."


Rejection of women, and disabled or imperfect men as priests:

Women were prohibited from the priesthood. Men who have bodily defects were also not allowed to become priests. This included a man who was blind or lame or a dwarf, or who had a broken nose, an extrafinger, a humped back, pimples, scabby skin, crushed testicles, etc.
Leviticus 21:16-23 "...Whosoever he be of thy seed in their
generations that hath any blemish, let him not approach to offer the bread of his God. For whatsoever man he be that hath a blemish, he shall not approach: a blind man, or a lame, or he that hath a flat nose, or any thing superfluous, Or a man that is brokenfooted, or brokenhanded, Or crookbackt, or a dwarf, or that hath a blemish in his eye, or be scurvy, or scabbed, or hath his stones broken;"


God killed Jews at Taberah:

During the 40 years of wandering through the desert, some Jews complained about their hard life. God heard the complaints, became angry, and destroyed some outlying parts of the camp, presumably killing the inhabitants:
Numbers 11:1 "And when the people complained, it displeased the LORD: and the LORD heard it; and his anger was kindled; and the fire of the LORD burnt among them, and consumed them that were in the uttermost parts of the camp."


God killed Jews at Kibroth-hatta'avah:

God had provided manna for the Israelites to eat in the desert. But the people found a steady diet of manna (and nothing else) to be intolerable; they missed meat. They wept because they no longer enjoyed the varied diet that they had enjoyed in Egypt. God was enraged. He caused quails to converge on the camp so that the Israelites would have plenty of meat. Afterwards, he killed large numbers of the people with a plague because of their complaining.
Numbers 11:10-34 "Then Moses heard the people weep throughout their families...and the anger of the LORD was kindled greatly; Moses also was displeased...And there went forth a wind from the LORD, and brought quails from the sea, and let them fall by the camp...And while the flesh was yet between their teeth, ere it was chewed, the wrath of the LORD was kindled against the people, and the LORD smote the people with a very great plague."


God killed 250 Jewish leaders and their families:

Korah, Dathan, Abiram and about 250 of the leaders of the Israelites decided that they wanted to abandon God's instructions and adopt a more democratic form of government. They complained to Moses about the status of the priesthood. They believed that the entire congregation is holy, and that the priests should not exalt themselves above the common folk. They also objected to Moses' status as a dictator. God caused the ground to open and swallow the four main leaders. They were and their families were killed and descended into Sheol, the underground caverns where the dead live a shadowy existence. God sent fire to burn alive the remaining 250 leaders, their wives and children.
Numbers 16:1-35 "Now Korah...and Dathan and Abiram...and On...rose up before Moses, with...250 princes of the assembly, famous in the congregation, men of renown: And they gathered themselves together against Moses and against Aaron, and said unto them, Ye take too muchupon you, seeing all the congregation are holy, every one of them, and the LORD is among them: wherefore then lift ye up yourselves above the congregation of the LORD?...And the LORD spake unto Moses and unto Aaron, saying, Separate yourselves from among this congregation, that I may consume them in a moment...And it came to pass...that the ground clave asunder that was under them: And the earth opened her mouth, and swallowed them up, and their houses, and all the men that appertained unto Korah, and all their goods. They, and all that appertained to them, went down alive into the pit, and the earth closed upon them: and they perished from among the congregation. And there came out a fire from the LORD, and consumed the 250 men that offered incense."


God sent a plague which killed 14,700 Jews:

Following the mass murder of 254 leaders and their families, almost all of the Israelites complained about the terrible loss of life among these holy people. God was displeased and sent a plague which killed almost 15,000 Israelites.
Numbers 16:41-49 "...all the congregation of the children of Israel murmured against Moses and against Aaron, saying, Ye have killed the people of the LORD...And the LORD spake unto Moses, saying, Get you up from among this congregation, that I may consume them as in a moment. And they fell upon their faces. And Moses said unto Aaron, Take a censer, and put fire therein from off the altar, and put on incense, and go quickly unto the congregation, and make an atonement for them: for there is wrath gone out from the LORD; the plague is begun...And he stood between the dead and the living; and the plague was stayed. Now they that died in the plague were 14,700, beside them that died about the matter of Korah."


God orders genocides:

The Israelites had exterminated the Amorites. God ordered them to also wipe out the Bashan in the same way.
Numbers 21:34-35 "And the LORD said unto Moses, Fear him not: for I have delivered him into thy hand, and all his people, and his land; and thou shalt do to him as thou didst unto Sihon king of the Amorites, which dwelt at Heshbon. So they smote him, and his sons, and all his people, until there was none left him alive: and they possessed his land."


God sends plague which killed 24,000 Israelites:

While in Shittim, all of the Israelites began to follow another
religion. They worshipped Baal, a God of the Moabites and other Pagan tribes. The Biblical text is a bit confusing here. It says that: God ordered Moses to kill all of the tribal leaders of Israel as punishment. God sent a plague as punishment. Moses ordered that all Israelites who had worshipped Baal be executed. (Since all of Israel was involved in Pagan worship, this would presumably include everyone.) A young man, Phinehas, saw an Israelite man, Zimri, with a Moabite woman, Cozbi. Phinehas became enraged that one of their men had become involved with a woman from another tribe. He murdered both of them with a single spear thrust. God was pleased with this action and stopped the plague at the point that 24,000 had died.
Numbers 25:1-18 "And Israel abode in Shittim, and the people began to commit whoredom with the daughters of Moab. And they called the people unto the sacrifices of their gods: and the people did eat, and bowed down to their gods. And Israel joined himself unto Baalpeor: and the anger of the LORD was kindled against Israel. And the LORD said unto Moses, Take all the heads of the people, and hang them up before the LORD against the sun, that the fierce anger of the LORD may be turned away from Israel. And Moses said unto the judges of Israel, Slay ye every one his men that were joined unto Baalpeor. And, behold, one of the children of Israel came and brought unto his brethren a Midianitish woman in the sight of Moses, and in the sight of all the congregation of the children of Israel, who were weeping before the door of the tabernacle of the congregation. And when Phinehas, the son of Eleazar, the son of Aaron the priest, saw it, he rose up from among the congregation, and took a javelin in his hand;
And he went after the man of Israel into the tent, and thrust both of them through, the man of Israel, and the woman through her belly. So the plague was stayed from the children of Israel. And those that died in the plague were twenty and four thousand. And the LORD spake unto Moses, saying, Phinehas, the son of Eleazar, the son of Aaron the priest, hath turned my wrath away from the children of Israel, while he was zealous for my sake among them, that I consumed not the children of Israel in my jealousy. Wherefore say, Behold, I give unto him my covenant of peace:"


God orders genocide of the Midianites:

God ordered that the Midianites be exterminated because of their religious beliefs and practices. The Israeli army kills all of the Midianite men, and took the women and children captive. Moses was angry that the army had taken the women captive instead of murdering them. He ordered all of the boys and any women who were not virgins to be killed in cold blood. Virgin girls, some 32,000, were allowed to live.
Numbers 31:7-41 "And they warred against the Midianites, as the LORD commanded Moses; and they slew all the males...And the children of Israel took all the women of Midian captives, and their little ones, and took the spoil of all their cattle, and all their flocks, and all their goods...Moses was wroth with the officers of the host...And Moses said unto them, Have ye saved all the women alive?...Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him. But all the women children, that have not known a man by lying with him, keep alive for yourselves."


God orders extermination of residents of Canaan:

Canaan is an area which includes modern-day Israel, the occupied territories, and part of Lebanon and Syria. Its borders are defined in Numbers 34:1-12. The Canaanites were well established there. According to the Bible, Joshua led the Israeli army into Canaan killing any adults and children who did not vacate the land. God's motivation for ordering this destruction appears to have been the
religion of the Canaanites. Their carved stones, molten images, and open-air religious sanctuaries were to be desecrated and destroyed. Much of the book of Joshua describes the carnage.
Numbers 33:50-52 "And the LORD spake unto Moses...saying...When ye are passed over Jordan into the land of Canaan; Then ye shall drive out all the inhabitants of the land from before you, and destroy all their pictures, and destroy all their molten images, and quite pluck down all their high places:"


God hardened the hearts of the Canaanites so that they would resist the invasion of the Israelites:

Joshua 11:19-20 "There was not a city that made peace with the children of Israel, save the Hivites the inhabitants of Gibeon: all other they took in battle. For it was of the LORD to harden their hearts, that they should come against Israel in battle, that he might destroy them utterly, and that they might have no favour, but that he might destroy them, as the LORD commanded Moses."


All of the people in Jericho men, women and children, were killed or murdered:

Joshua 6:21 "And they utterly destroyed all that was in the city, both man and woman, young and old, and ox, and sheep, and ass, with the edge of the sword." The king of Ai was kidnapped and later murdered. All of the rest of the inhabitants, young and old, were killed or murdered.
Joshua 8:25 "And so it was, that all that fell that day, both of men and women, were twelve thousand, even all the men of Ai."


Five armies from southern Canaan joined together to fight the Israeli army, and were wiped out:

The five kings were captured and murdered in cold blood. The Israelites then attacked each of the cities in the area: Makkedah, Libnah, Lachish, Eglon, Hebron, and Debir. Every person was killed.
Joshua 10:28-39 "...Joshua took Makkedah...he let none remain: and he did to the king of Makkedah as he did unto the king of Jericho. Then Joshua passed from Makkedah, and all Israel with him, unto Libnah...and he smote it with the edge of the sword, and all the souls that were therein; he let none remain in it...And Joshua passed from Libnah...and smote it with the edge of the sword, and all the souls that were therein...Then Horam king of Gezer came up to help Lachish; and Joshua smote him and his people, until he had left him none remaining. And from Lachish Joshua passed unto Eglon...and all the souls that were therein he utterly destroyed that day. And Joshua went up from Eglon...and smote it with the edge of the sword...and all the souls that were therein; he left none remaining...he...destroyed it utterly, and all the souls that were therein. And Joshua returned, and all Israel with him, to Debir...and utterly destroyed all the souls that were therein; he left none remaining:"


An alliance of many kings joined to fight Joshua. They were defeated:

The Israelites "did not leave any that breathed."
Joshua 11:4-15 "And they went out, they and all their hosts with them, much people, even as the sand that is upon the sea shore in multitude, with horses and chariots very many. And when all these kings were met together, they came and pitched together at the waters of Merom, to fight against Israel...And the LORD delivered them into the hand of Israel, who smote them, and chased them unto great Zidon, and unto Misrephothmaim, and unto the valley of Mizpeh eastward; and they smote them, until they left them none remaining. And Joshua at that time turned back, and took Hazor...And they smote all the souls that were therein with the edge of the sword, utterly destroying them: there was not any left to breathe: and he burnt Hazor with fire. And all the cities of those kings, and all the kings of them, did Joshua take, and smote them with the edge of the sword, and he utterly destroyed them, as Moses the servant of the LORD commanded. Joshua...left nothing undone of all that the LORD commanded Moses."


Two kings on the east side of the Jordon river, and 31 kings on the west side were killed and their cities destroyed:
Joshua 12: 1-24 "Now these are the kings of the land, which the children of Israel smote, and possessed their land on the other side Jordan toward the rising of the sun, from the river Arnon unto mount Hermon, and all the plain on the east: Sihon king of the Amorites...Og king of Bashan...And these are the kings of the country which Joshua and the children of Israel smote on this side Jordan on the west [list deleted]...all the kings 31."


God threatens to kill men who allow their children to marry outside their group:

God forbade men of ancient Israel from allowing their sons and daughters from marrying people from the surrounding Pagan nations - people who were not part of Israel.
Deuteronomy 7:3-4 "Neither shalt thou make marriages with them; thy daughter thou shalt not give unto his son, nor his daughter shalt thou take unto thy son. For they will turn away thy son from following me, that they may serve other gods: so will the anger of the LORD be kindled against you, and destroy thee suddenly."


Destroy the temples of other religions:

No places of worship are to be tolerated; all are to be destroyed.
Deuteronomy 12:2-3 "Ye shall utterly destroy all the places, wherein the nations which ye shall possess served their gods, upon the high mountains, and upon the hills, and under every green tree: And ye shall overthrow their altars, and break their pillars, and burn their groves with fire; and ye shall hew down the graven images of their gods, and destroy the names of them out of that place."


God permits a human sacrifice:

Jephthah led the fight against the Ammonites. He promised God that if he was victorious that he would conduct an human sacrifice, ritually murdering the first person to meets him on his return to his house. God gives him the victory, and does not intervene when Jephthah ritually murders his only daughter.
Judges 11:30-39 "And Jephthah vowed a vow unto the LORD, and said, If thou shalt without fail deliver the children of Ammon into mine hands, Then it shall be, that whatsoever cometh forth of the doors of my house to meet me, when I return in peace from the children of Ammon, shall surely be the LORD's, and I will offer it up for a burnt offering...And Jephthah came to Mizpeh unto his house, and, behold, his daughter came out to meet him with timbrels and with dances: and she was his only child...And it came to pass at the end of two months, that she returned unto her father, who did with her according to his vow which he had vowed.”

Prejudice, hatred and retaliation by God against individuals and religious groups
http://www.religioustolerance.org/intol_bibl1.htm