Dinesh D'Souza - The best defense is a good offense
Atheism was always a side-effect of both Communism and Nazism. Take Communism for example. The main doctrine of communism has to do with class struggle and economic equality. The initial Bolshevik terror had to do with killing of "class enemies". Stalin's purges had nothing to do with ideology at all, as is well documented. He was simply killing anyone whom he perceived as a potential threat.
So, what makes people commit genocide - religion or atheism? My suspicion is that it is neither. Mass killing is part of human nature. It is as old as humanity. Mainly it has to do with identifying the "Other" and then eliminating it. The reasons may be ethnic, religious, economic or social or all of the above.