In 1938 Hitler declared; "I believe today that I am acting in the sense of the Almighty Creator. By warding off the Jews I am fighting for the Lord's work."
"Article 24 of Hitler's Nazi party programs calls for "Positive Christianity". Among the 25 points of the core values of this new Christianity, as explained by German philosopher Ernst Bergmann in 1934, is point number six which states: "The German religion is a religion of the people. It has nothing in common with free thoughts, atheist propaganda, and the breakdown of current religions."
None of the crimes that the Nazis carried out were done in the name of atheism. Most of the German population were Protestants or Catholics (including Hitler himself who never declared himself atheist) and the Nazis and fascists in Italy maintained a close relationship with the Vatican. You might as well say, it was the Nazis liking for jazz music that made them kill, rather than atheism.
"While it is true that Joseph Stalin (1879-1953), Mao Zedong (1893-1976) and Pol Pot (1925-1998) were all atheists, this is not the only thing they have in common. They were also men, political leaders and communists. Merely citing common denominators does not establish the cause of their actions. It is important to consider what was the main driving force in their committing atrocities against their own people.
If we look in detail at the horrors committed by these men - Stalin, Mao Zedong and Pol Pot - we will see that the atrocities were the direct result of Marxist-communist doctrines that had nothing to do with atheism."
Stalin's attrocities were as a result of the farm collectivisation programme and his paranoia about his political opponents. Nobody was killed for opposing atheism.
Mao's attrocities were similar; "The idea that individual ownership of capital is evil caused many of the landlords to be murdered. Then the belief that collectivization would solve the problems of famine in the country actually exacerbated it. Finally intolerance of opposing views, or of people who were deemed capable of holding opposing views, resulted in the execution of many "intellectuals". These were heinous crimes - but communism and despotism, not atheism, were to blame."
"Pol Pot had a deep seated hatred of "intellectuals" and summarily executed many of these. These "intellectuals" include anyone with a college education, civil servants from the previous regime, Buddhist monks, Muslim leaders, Christian clergy, teachers and practically all members of the middle class. However the bulk of the three millions deaths he was responsible for happened in almost the same circumstance as Mao's "Great Leap Forward" - to try and achieve an ideal classless society where everybody is a plebian farmer!"
Quotes taken from here.