When atheists were in control of governments, in the Communist world, there was plenty of mass killing. You can certainly be a racist with or without religion. (Hitler didn't exterminate Jews for religious reasons, for examples). Human nature, not religion, seems to be the reason why we do evil things to one another. Ideologies, religious or otherwise, can serve as a pretext. But at least with Christianity, killing without justification is against one of the Ten Commandments.
If you thought that the worst thing in the world was religion, you thought the end justified the means, and you had the power to do something to get rid of it, you could decide to commit atrocities to free the world of religion. Why couldn't this happen? What is there about the rejection of religion that would prevent this? Doesn't all the evidence point the other way? Why think atheism would give us all nothing to kill or die for?
No one has ever come close to explaining to me how the abandonment of religion would do anything to eliminate man's humanity to man.