They kill people because they consider some humans to be superior than others (like Hitler) or because they can do so. Their moral judgements were wrong because they didn't subscribe to better moral standards like in (most) religions.
The point is without religion one's morality CAN be dangerous. Atheism doesn't give you guidelines about Morality and then Atheists have to look elsewhere to make moral judgements. Atheists can be vegetarians, humanists, philanthropist or misanthropes. A misanthrope atheist can easily justify killing someone he doesn't like too much.
One can make an case about Mao and Stalin being misanthropes because they justified the killing of thousands by their twisted moral standards.
God cannot come out of nothing . Similarly, morality cannot come out Atheism. So there is no way you can control the choice of morality.
I have been a former nihilist and believed personally that after you become morally nihilist, you can do anything - even kill someone if no one is watching :
Well interesting point, I am also not against religions with philosophy of live and let live. Unfortunately most of the religions are intolerent . Well you don't require religion for morality, Particularly in case of Dharmic religions which are more of cultures than religions, I am culturally hindu (brahmin) but atheist by belief, in Dharmic culture belief is personal matter between individual and god.