Religious people often try to blame atheists for the evils of Nazism and Stalinist communism, as the Pope did not very long ago in a speech in the UK that linked atheists with the Nazis. In the case of the Nazis, that's grossly unfair, as Nazism was not atheistic and Hitler hated atheists along with Jews, homosexuals, and his various other imagined enemies. Hitler repeatedly made clear that he thought God or divine Providence was on his side. There is plenty of information about this, including a fair, thoughtful, and sensitive discussion in The God Delusion by Richard Dawkins.
By contrast, Stalin really was an atheist, so if you want to attack atheism and claim that it leads to horrors, that might be a promising place to start. But here's the thing: although I think that all sorts of god-belief are untrue, I don't think that they are all terribly or similarly harmful, and nor do I think they are uniquely harmful. For example, pagan polytheism may have encoded some of the less savoury aspects of ancient societies, such as the frequent misogyny and male fears of women's power, but by and large it was tolerant and certainly not apocalyptic or totalitarian. Whatever its faults, it did not have the same kinds of problems as the more modern sorts of monotheism such as Christianity and Islam.
By contrast, the sorts of Marxist-Leninist revolutionary communism embraced by Stalin and Mao did have many of the same problems as those monotheisms, which they imitated in many ways. In particular, they had the same extreme authoritarian tendencies. The thing is, these were comprehensive and apocalyptic belief systems. Though not positing the traditional Abrahamic God, they tended to create their own God - history with a capital-H - and to tell their followers that History was on their side.
This way of thinking is dangerous: once you think that you're acting in the service of God or History, you can be tempted to do terrible things. We have very good reason to question the authority of all forms of comprehensive, apocalyptic dogma, whether they are monotheistic or formally atheistic. If threats to our freedom currently emanated mainly from formally atheistic kinds of comprehensive apocalyptic dogma, I'd be saying very loudly that we must question these and their claims to moral and epistemological authority.
However, that is not the historical situation we are in. The Cold War has been over for a long time; as far as I can see, even China no longer subscribes in any serious way to a comprehensive body of apocalyptic dogma (though it certainly remains authoritarian); and the undoubted dangers of Marxist-Leninist revolutionary communism are about the least of our current worries.
But yes, political liberals like me are not concerned solely about the dangers of theistic dogmas. Any kind of comprehensive, apocalyptic dogma is a danger to our liberties and likely to be a source of atrocities if its adherents gain power. I get very impatient when my efforts to question the authority of religion receive the reply that terrible things were also done in the name of atheism. No they weren't: by and large they were done in the name of a quasi-religion that had its own prophets, holy books, apocalyptic view of history, and comprehensive body of dogma. All such systems merit scrutiny, but since the Cold War ended about 20 years ago, the greatest threats come from theistic systems; those are the ones we should be focusing our criticism on for the moment.
That doesn't mean that secular political liberals are never tempted to develop their ideas into comprehensive schemes with totalitarian tendencies and an element of apocalypticism. That could happen. We all need to scrutinise ourselves constantly to ensure that we're not going down that path. When I've spoken to religious groups, I've asked them to scrutinise themselves for those tendencies, but I've also pointed out that everyone in the room, including me, should do that constantly. By and large, though, secular political liberals are about the last people who'll be building and imposing comprehensive, apocalyptic systems with totalitarian tendencies. That's because we're aware of the dangers of all such systems and our life mission, to put it a bit melodramatically, is to oppose them.
It's worth reminding ourselves of the temptations now and then, of course, but it's also worth our while to tell people who compare us to Hitler, or even to Stalin, that they don't know what they're talking about.