It's hardly surprising that insane totalitarians would go to war against something that threatens to potentially, let alone actually, be a power structure they do not control. But I don't see this as a product of atheism. They would ideally, I think, want a religion under their control, as the Russian Orthodox Church increasingly seems content to be. The Nazis weren't atheist, but they sure as hell didn't tolerate any Christians letting Christianity get in the way of Nazism.
But if they can't create a religion, and can't find one willing to knuckle under, sure, they'll throw stubborn religionists on the same pyre as all the other dissidents.