There has never been massive slaughter of Christians in specific because of their faith. Just because the person who ordered it did not believe in god does not mean that that was their motive to do so. Then again, there's the opposite...
Speaking of which, more about national socialist Germany:
“We were convinced that the people needs and requires this faith. We have therefore undertaken the fight against the atheistic movement, and that not merely with a few theoretical declarations: we have stamped it out.”
-Adolf Riddler, in a speech in Berlin on 24 Oct. 1933