Peresozo makes a good point and mentions the theist charge that atheists are unable to account for evil. But is the atheist account really deficient? And against what standard could we call it deficient?
Peresozo's comment raises several fundamental questions. We want to know not only why there's evil, but how to think about it and what to do about it. A simple causal account of evil is itself deficient; what we really want is an account of ethical thinking we can use in practice. Thus we can recast the question: Are atheistic accounts of practical ethical thinking deficient? Are theistic accounts sufficient?
Taking the second question first, I submit that theistic accounts of ethical thinking are themselves deficient, consisting of at best content-free platitudes, sometimes incoherence, and at worst moral nihilism. The theistic causal accounts of evil entail either that God is not omnipotent or that we don't understand good and evil; in either case, the accounts don't help our ethical thinking at all.
The "free will" defense to the Problem of Evil entails that God cannot or chooses neither to prevent evil nor promote good: We are, rather, free to choose one or the other. This is not a bad defense of theism, but removes God from our moral reasoning, making morality our problem, not God's.
The "greater good" defense entails that although some things appear evil, they are really in the service of a greater good. In which case, all our language condemning and praising acts seems at best entirely metaphorical; a realistic view would entail a Panglossian approval of everything. We can still make pseudo-moral judgments—and it's part of the greater good that we do so—but such judgments are not about good and evil per se (since everything is for the greater good) but about who-knows-what else. And again we are back to figuring out for ourselves what all this ethical thinking is really all about.
Both defenses throw morality back into the realm of purely human reasoning. They may (in the usual Swinburne-style non-explanation explanation) "account for" what we call evil in the sense of explaining why there is evil, but neither defense at all accounts for our actual practical moral reasoning. So it's not clear that there's any standard at all against which the atheistic account might be judged "deficient".
Of course, atheism per se does not do anything but describe a lack of belief in a God. Atheism just constrains explanations and thinking, but as noted above, it does not place any more constraints on our moral reasoning than theism in the face of the Problem of Evil.
There are two ways atheists tend to look at the world: naturalistic physicalism, a fundamentally monistic view, and naturalistic dualism: That the universe is composed of physical stuff (the stuff that we ends up interpreting as matter and energy) and, in this context, ethical stuff (probably a subset of mind stuff). The dualistic view has the advantage of very simply accounting for the words "good" and "evil" as naming this ethical stuff. However, I've never been persuaded to this view: This ethical stuff or mind stuff seems very elusive.
Scientific physicalism entails that our moral reasoning is about something physical: Either some kind of physical substance or some physical arrangements of this substance. Since there doesn't appear to be any kind of good or bad matter or energy or quantum states, we have to look to arrangements. And the obvious place to look for these good and bad arrangements is to look at those arrangements of matter we call minds, which entails meta-ethical subjective relativism, that our ethical thinking and language fundamentally names states of mind.
Peresozo raises the obvious objection: This view entails that our judgment of Hitler (or Cho) is merely that their actions are "not to [our] taste." But why should this be an objection at all?
First of all, I the characterization of ethical beliefs as "taste" is misleading, and trades on the equivocation fallacy of similarity entailing identity. According to MESR ethical beliefs are, similar to tastes, subjective, but "tastes" are precisely those subjective beliefs we do not condemn differences in others. It is less prejudicial to say that our judgment of Hitler is that his actions meet with our violent subjective disapproval.
Thus we can say that if Hitler's acts did not meet with our violent subjective disapproval, we would not call them unethical. Well, of course. But so what? His actions do in fact arouse our violent subjective disapproval. Why should we be concerned with the acts of fantasied possible worlds or alien species in which the actual here-and-now facts do not apply?
As Peresozo notes, if ethical beliefs are about mental states, there will be conflicting ethical beliefs. It is a fact that some people approve of Hitler's actions. It is a fact that millions (if not hundreds of millions) of Muslims actually cheered the attacks of 9/11, indicating their hearty approval. Millions (if not hundreds of millions) in America and the West naturally disapprove of both Hitler and bin Laden. According to MESR, none of these people are objectively mistaken: Since our ethical beliefs do not fundamentally name facts about objective (outside the mind) reality, there is nothing to be mistaken about.
How are we to deal with such conflict if objective truth discourse is simply inapplicable? Well, we can deal with ethical conflict in precisely the same way that we do in fact deal with it here and now: Propaganda and negotiation. Democracy. At worst imprisoning or killing people with objectionable beliefs and fighting wars. Institutions and techniques that do not fundamentally use objective truth discourse.
Given this view, the account of evil offered by naturalistic physicalism is trivial: We evolved minds which make value judgments; to the extent that we make different value judgments, a person with one value judgment will label as "evil" the differing judgment in another. There is no "problem" of evil, there's no unexplained phenomena, and naturalistic physicalism entails precisely what we do in fact see: that we use propaganda and negotiation discourse, rather than objective truth discourse, to resolve our ethical conflicts.
The bar that theistic morality raises to atheistic ethical discourse is entirely illusory. The ethical bar, however, that atheistic philosophy raises to theism is considerable.
 I prefer the term naturalistic physicalism to scientific materialism; if quantum mechanics makes anything clear it is that our ordinary intuitions about matter are not applicable to fundamental physical reality, and naturalism is a superset of scientism, avoiding the connotation of science as a process that relies only on public facts. I personally tend to use science and naturalism more-or-less interchangeably.
 I.e. whatever physical characteristics of our brains on which our abstract concepts of states of mind supervene.
 Tastes are those beliefs we also do not condemn in ourselves. Internal ethical conflict is as important a consideration as external conflict; I'll write more on this topic later.
 Note that for any Abrahamic theist who gives any intrinsic weight to scripture, which in both the Old Testament and the Koran has God explicitly ordering genocide, the condemnation of Hitler is not a condemnation of his acts themselves, but only of his authority to act in such a manner. Again we see that at least Abrahamic theism does not raise much of a bar that atheistic ethical discourse must surpass.
 Except in the senses that we want to determine what in physical reality what it is we're actually subjectively judging, and to determine what people's ethical beliefs actually happen to be.