Hitler claimed to be a christian. Mao and Stalin killed people for 'the greater good' or something like that. I'm actually hard pressed to find any incidents where a bunch of atheists killed people for being religious.
If anything Hitler was against Christianity, but felt that the time to deal with Christians was to be left to a time well after the other "lesser races" were dealt with. There clearly was anti-Christian bias in some of the letters and writings of Hitler, and a sort of psuedo-religious cult that came up in the form of Nazism that transcended Christianity.
Certainly the anti-Jewish sentiment in Nazism was not grounded in Christianity, but rather in something far more profound and a sort of religion in its own right.
As for being hard-pressed to look for any incident where a bunch of avowed atheists have explicitly killed those harboring religious beliefs as their only "crime"? I don't think you have looked hard enough. Millions have died at the hands of atheists, or at least governments that have sought explicitly to purge religious thought. Both Mao and Stalin were involved in that killing, and both professed official atheism. It wasn't merely "the greater good", but that was indeed the rationale. It also involved more than just these two men.
Even today in China, if you tried to open a church or express your religious beliefs in a public manner without formal state approval you will get arrested and possibly even killed on the spot for what in most "western" nations would be considered a non-violent protest. I'm not talking twenty or forty years ago, I'm talking today. People are still being killed today in the name of atheism, or because they don't disavow their religious beliefs.