Hitler was an avowed pagan with interest in Hinduism and Tibetan Buddhism – he hoped to amalgamate these into a religion with himself at the center. He worshipped Odin. He made this very clear to those near him and occasionally played to the Christian crowd when convenient, turning around to speak at his friends’ funerals and declare them to be in Valhalla. He often denounced Christianity, and persecuted huge numbers of Christians for refusing to alter their doctrines little-by-little and morph into his invented religion. The resistance was huge among both Protestants and Catholics, and clergy were well-represented in it.
But then, these “Christian atrocities” do seem to be a lot like the grey dots between black squares on a white background – it’s positively blanketed with them, always with the exception of whichever one you focus on at the moment. One, the Holocaust e.g., turns out to be basically done by anti-Christians, resisted by Christians – another, such as the witch hunts, was started and done by laypeople, and the clergy were trying to stop the violence, not ordering it. Christian leaders passed laws against accusing anyone of witchcraft or vampirism, but the civil courts often didn’t heed these laws because crowds were demanding a witch hunt. Another, say, the first Inquisition, after all the inflated body counts are wafted away and only the facts remain, is smaller than the damage from a typical urban turf war anywhere today. And so on. Either not the scene we’ve heard so many expanding tales about after all, or not done by anyone to do with any major Christian church, or both, one by one these supposed Christian atrocities vanish when you look directly at them.
Pol Pot was a Buddhist, but his economic policies, the reason he was in power in the first place and his political system itself, all were against Buddhist as well as Christian rules. All these were a direct outcome of a group of 19th-Century intellectuals’ attempts to find a non-social-darwinist way of organizing a society where nothing was considered sacred.
Atheism doesn’t automatically prevent morality, but it does tend to imply pragmatism, which isn’t the same thing as morality.