When an atheist addresses the fact that religion has been used throughout history to justify hatred, oppression, injustice, genocide, murder, war and so on, the response from theists is almost universally the same; “You can’t fault the religion for the things that are done in the name of that religion. It’s not the religion that kills people” etc. Whilst I don’t deny that the abstract concept of religion itself cannot physically kill or harm people, that’s not the point. The abstract concept of racism, nazism, fascism, communism etc. cannot physically harm people either, but those concepts have undoubtedly been used to justify harm throughout history.
There are many instances throughout history in which people have justified evil using religion. The most recent pertinent example would be 9/11. I can say without a shadow of a doubt an atheist could never be convinced to fly a plane into a building full of innocent people. The hijackers were undoubtedly motivated by their religious convictions, they saw themselves as martyrs, and believed that they would be rewarded in paradise for their actions. If the concept of religion was absent from the world, then the chances are that the Twin Towers would still grace the New York skyline.
The abstract concept of religion did not hijack those planes, that is correct, but it did hijack the minds of the people who did.
Anti-Semitism is most commonly associated with Nazi Germany, but it has its roots much earlier than that, and was directly justified by Christian scriptures. The Christians held the Jews accountable for the death of Jesus. In their eyes his blood was upon them and their children, as written in the Gospel of Matthew:
“So when Pilate saw that he was gaining nothing, but rather that a riot was beginning, he took water and washed his hands before the crowd, saying, “I am innocent of this man’s blood; see to it yourselves. And all the people answered, “His blood be on us and our own children!” – Matthew 27:24-25
Anti-Semitism is justified in other parts of the Bible, take this quote from Thessalonians for example:
“For ye, brethren, became imitators of the churches of God which are in Judaea in Christ Jesus: for ye also suffered the same things of your own countrymen, even as they did of the Jews; who both killed the Lord Jesus and the prophets, and drove out us, and pleased not God, and are contrary to all men; forbidding us to speak to the Gentiles that they may be saved; to fill up their sins always: but the wrath is come upon them to the uttermost.” – Thessalonians 2:14-16
Once Christianity became the state religion of Rome in 312 CE under Constantine, hatred and oppression towards Jews became extreme. Laws were passed that revoked many of the civil liberties previously granted to Jews. Jews were excluded from the military, from holding high office, and were forbidden to proselytize or have sexual relations with Christian women – under penalty of death. The Justinian Code of the 6th century declared the legal status of Jews null and void, outlawed the Mishnah, and made disbelief in the resurrection a capital offence . I have to ask, would this oppression and injustice have existed without the religious justification?
Here’s another example of a Biblical commandment that was used to justify evil:
“Thou shalt not suffer a witch to live.” – Exodus 22:18
Witches, despite not existing, were persecuted for some three hundred years, and those tortured and murdered under suspicion of this imaginary crime number at around 40,000 to 50,000 . Again I ask, without the religious justification, would this have happened?
Then you have the inquisition, justified by verses such as this:
” If you hear it said about one of the towns the LORD your God is giving you to live in that troublemakers have arisen among you and have led the people of their town astray, saying, “Let us go and worship other gods” (gods you have not known), then you must inquire, probe and investigate it thoroughly. And if it is true and it has been proved that this detestable thing has been done among you, you must certainly put to the sword all who live in that town. You must destroy it completely, both its people and its livestock. You are to gather all the plunder of the town into the middle of the public square and completely burn the town and all its plunder as a whole burnt offering to the LORD your God. That town is to remain a ruin forever, never to be rebuilt,” – Deuteronomy 13:12-16
Countless people were horrendously tortured and killed during the inquisition, without the religious justification this would not have happened. I could go on citing examples, such as how the Bible was used to justify slavery , Manifest Destiny  and many others. Now, I am not arguing that all religious people are advocates of Anti-Semitism, torturing witches and heretics, slavery etc, what I am saying is that religion was undoubtedly used to justify these things, and in most cases, without the religion these actions would have had no justification whatsoever.
I do not deny that religion can motivate people to do good, but it can also give overwhelming justification to evil – when you feel that you are justified in doing something by the omnipotent creator of the universe, you have a real problem. As Stephen Weinburg said:
“Religion is an insult to human dignity. With or without it, you’d have good people doing good things and evil people doing bad things, but for good people to do bad things, it takes religion.”
No one is blaming the abstract concept of religion for harming people, the problem with religion is that it is often used to justify evil, and for that reason it is highly dangerous, and should be opposed.
 Wistrich, Anti-Semitism pages 19-20
 R. Briggs, Witches and Neighbours: The Social and Cultural Context of European Witchcraft page 8