Okay, I have been seeing a lot of this come up lately, and it grows increasingly annoying because it obvious that it is a hell of a lot easier to ask, remember, and regurgitate across the intertubes than it is to come up with a clear and concise response to why it is more than a little off kilter. The basic idea is this: atheism is no better/worse than Christianity because the worst crimes and atrocities committed by Christians have only death tolls in the thousands, but the atheists Stalin, Mao, and Pol Pot all killed a number of people in the millions.
Let me just point out the problems, step by step. The first little complaint is that "atheism" cannot be equated to Christianity as an ideology, in that atheism is simply the lack of belief in god(s) and has no other common doctrine or conclusions attached to the title. As such, there is very little uniting atheists together, and very little that defines them as being similar, and, as such, any given atheist has less in common with another atheist than a Christian would have in common with a Christian (even despite the heavily sectarian nature of the religion), due to the large amount of doctrine that they both are exposed to, are influenced by, and tacitly accept. Atheists have no such comparable exposure or adherence to common ideas, and, as such, atheism in of itself cannot be as connected to the activities of any given atheist as it could be for any given Christian. I know this sounds unfair, and undemocratic of me, but I think it stands to reason that people who all believe in the existence of God, the veracity of the Bible, the divinity of Jesus, the necessity of his moral law (whatever those morals may be...), and who regularly interact with those who share those beliefs in settings focused explicitly on them have slighty more ideological connections to one another than the rare, insular people whose only common belief is that they have no belief in the religions that surround them.
The second problem is related to the first: that, even though these three dictators were all atheists, what defined their actions and mindsets more than simple non-belief in gods alone were the ideologies of communism to which they subscribed (and abused in order to attain oppressive totalitarian regimes). There was far more similarities in regards to their political ideologies than anything to could be said about atheism alone.
The third issue is both of a general defense of any set of ideas, beliefs, or actions that are challenged due to an alleged connection to a set of horrifying events. Though it is tempting to leap to judgment when a (presumably) clear correlation between some kind of ideology's prominence in a society or many societies and horrible events occuring in those locations, it is pertinent to try to reserve judgment unless you have seen that the ideology can and has influenced such behavior in several different socio-political climates, varied in time and location. The more it seems to occur across different times and regions, the more confidently we can blame the ideology itself, rather than underlying problems in the population, societal structure, economy, etc., which is presumably unrelated to the ideas criticized. And, unfortunately, the atrocities of communist regimes are relatively confined to a few struggling nations within the early to mid 20th century. Whether these nations alone reflect upon an inherent evil in communism or atheism, one could hardly say with honesty.
The fourth issue is whether the massive death toll somehow makes Christianity's own death toll from the witch trials, Crusades, Inquistion, etc. less significant. There are few problems with this. The first is that the three atheistic regimes did not engage in formal warfare, which is what constitutes an "atrocity", apparently, whereas this was the primary fashion in which Christianity went about killing a majority of the lives that could be tallied up against it. The problem is that we somehow dismiss the warfare as justifiable and beyond reproach (in fairness, I do not mean to suggest that Christianity in of itself was behind every war of Christian nations, but I simply mean to express that one need not spill the blood of many dissidents when you are sending off your own to kill and die for the sake of glory, satisfying the desire for violence and power in a more "acceptable" fashion). The second is that Stalin/Mao/Pol Pot had a much larger population to work with and, as such, it is a little underhanded to suggest that the failure of Christians to kill millions within the confines of a decade in the Middle Ages, as these three have done in the 1900's, somehow reflects upon some form of restraint. The third is related to the second: Stalin/Mao/Pol Pot not only had a larger crop of potential victims than Christianity had in its more impressionable years, but they also had much more efficient modes of execution. Even if the population had been identical to today back during the Inquisition, the Inquisition would still fail to have a significant death toll comparable to the atrocities of the three communist regimes without the Industrial era tools, transportation, and weaponry to do it (to say nothing of the fact that the Inquisition would need to focus more on execution and less on torture to compete).
So, to put it concisely, atheism is not detailed, consistent, or universal enough in its implications to be blamed for the actions of Stalin, Mao, and Pol Pot; what is more more relevant to the Big Three's behavior is communist ideology itself (which, even there, they deviate); one should not dismiss any set of ideas or beliefs as the direct cause of certain events without seeing that there is not something else at work (the fact that most successful and peaceful European countries of our day and age are atheistic helps to show that the assumption that atheism itself leads to these atrocities is flawed); and Christianity's atrocities are not entirely mitigated by the fact that they have lower total deaths attributed to them, given the fact that those atrocities may have been much larger in scope if given the population size and technology of the nations that they are being compared to.
All in all, this little argument, though deceptively convincing, is blatantly unfair and is a glorified illustration of jumping to the conclusion of correlation implying causation. As such, this argument is suitable as a rebuttal to a similarly unfair jump in logic of trying to cast doubt upon the entire precipice of Christianity by touting about a few acts of violence of centuries past. When it comes down to it, and you get beyond the false appeal of an argument from consequences, none of the tenets of Christianity, nor the arguments of atheism, are swayed in the slightest. They merely sit, ignored, as we entertain ourselves with horrific distractions.