Hitler was very much a Christian.

Atrocities are committed when individuals claim themselves and their ideas to be above everyone else. This is true of the religious (pharaohs, popes, etc) as well as the non-religious (Stalin, Castro, etc). Since the atheist/agnostic movement is relatively young compared to the history of religion, there have been many more opportunities for religious leaders to rise and commit atrocities. Invoking God has proven a popular way to gain support for these acts because no burden of proof is necessary. God's word is absolute, and therefore anything done in his name is justified. In secular societies, the ruler(s) must present justification for why such acts should be committed, and this justification is generally based on flawed logic and/or suppression of dissent. Although certainly not impossible (as history shows), I think it is more difficult to achieve. The key to preventing such atrocities is an open society and education of the people, with strong and constant debate based on reason and logic. This is impossible in strict religious societies because the belief in a higher power and a value system based on untestable ideas and ancient texts prevents any debate that may challenge it. It is at it's heart authoritarian. So while atrocities can be committed by the religious and the non-religious, religious societies tend to have less of the societal constructs necessary to prevent them, and thus makes them more susceptible.