I am sure many secular people have heard the Hitler, Stalin, and Mao argument against the atheist position. I really do hate judging atheists as a whole based on three people as if atheists are naturally murders. Even if we grant that average atheists have done more harm, that does not prove that atheist leadership will lead to genocide.
But there is a better argument against this evil atheist dictatorship argument, and that is to focus on reasoning rather than beliefs. Religions typically obsess about belief, not the path to those beliefs. For instance, regardless of how irrational the reason a Christian believes in Jesus's godhood, it is considered completely fine by Christian standards. If we look closely at the reasoning of an atheist that is not Mao or Stalin, we realize how important the view behind how reasoning should be done is. For example, take my view:
When I fight for my right to be free from religion, I also fight for the right for other people to have their own religious beliefs of their own choice.
If I take away the right to believe as you wish, I will be carrying out the same injustice that I blame the theocrats of enforcing through violence and fear.
If I accept that people ought to think for themselves, I must accept that people will adopt positions that I think are wrong, even absurd.
My hope is that free, open discussion will lead to self-regulation of ideas, so that the mainstream is not crazy and the values of other opinions won't become violent over disagreements on issues like religion.
I do not trust even an enforced atheistic regime because I do not believe in atheism as an absolute. My core philosophy is a methodology that force undermines. If you cannot use reason to reach your beliefs because force and fear determine what you believe, then even an atheistic conclusion is unjustified. The only justified conclusions are those thought through and with the evidence taken into consideration.
The methods of evaluation are known as science and some are still in debate to this day.
Even atheists who seek to undermine freedom of thought and neutrality in government with respect to conclusions (not methods) are my ideological opposition.
Atheists who think of humans as divisible into the categories of 'Us' and 'Them' undermine the ethical position that you should seek the good for everyone, even those who cause harm, unless the situation becomes too desperate.
When you can only see those who disagree with you as enemies, you can no longer yourself reason with them. You have stopped yourself.
One should be glad to have someone to give them sincere and thoughtful criticism, for this generally means that the person has your best interests in mind. In some cases it would be even wrong for someone not to mention that you're wrong. One should seek the best arguments against their position because beyond just rational benefit, it is better to know you have been wrong than to continue ignorant in your folly.
How can one blame someone who sincerely tries their best to know, who legitimately reaches a conclusion based on the information they had, but reaches the wrong conclusion? Just like I cannot blame a child for believing in Santa in a world that tells her that Santa is real, a theist ought not blame me for not believing in a deity when after all investigation I could not find one single piece of evidence beyond dubious testimonials.
With these views that reflect the kind of values in freethought that led to my atheism, how could anyone reasonably compare the society I seek to Stalin or Mao's?