Arguments between theists and atheists make me think they're both missing the point. People have belief systems. If yours doesn't make you hurt anyone, it's fine by me, and it's even better if yours helps you do good things.
Agnosticism is concerned with the limits of knowledge. Atheism is concerned with the likelihood of belief. Epistemologically, I'm an agnostic. That is, I accept that absolute knowledge is impossible, and therefore there is a logical possibility, however minuscule, that something vaguely called God could exist. Philosophically, I'm an atheist, because knowledge doesn't have to be absolute to be good enough for everyday life, and I feel confident enough that no matter what we discover about life in the cosmic or subatomic realms, none of it will ever point toward the likelihood of the existence of a bipolar creator god with a prurient interest in the doings of human genitals. I am quite willing to bet my life on that. Pragmatically, I'm an anti-assholist, and since assholes are in plentiful supply on both sides of the argument, I tend to agree that the issue is hardly worth fighting about.
That said, Will is probably preaching to those without ears to hear, because the argument isn't so much about whether theists/atheists are incapable of doing good because of their beliefs. Most people can grudgingly concede that however stubborn and deluded their opponents are, they manage to live decent lives — for now. The worry is — to take the atheist perspective here for a moment — that theistic beliefs are an intellectual weak link. The chain of one's moral character might snap at precisely that point if the link is not replaced. If a theist is allowed to retain a vague, sentimental affection for Biblical platitudes or an open-mindedness toward the possibility of life after death, the rust might spread and their personality might give way under stress, allowing some atavistic sympathy for the harshest aspects of Deuteronomy or Leviticus to break through and take over. The argument is that incorrect beliefs are a disaster waiting to happen, and both sides will patiently wait a lifetime, if need be, to claim vindication. As with God's existence, even a fraction of a possibility can inspire faith.
But intellectuals, both secular and religious, always overvalue the importance of rational principles as opposed to simple, intuitive empathy. The power of logical necessity compels you! Except, in practice, it doesn't. People cheerfully contradict themselves all the time. Faith or the lack thereof tends to serve as a mere rationalization for what are, deep down, issues of basic character. Kind people can be attracted to the soft parts of Christianity and assholes can be attracted to the supercilious parts of atheism. Decent, humane people do not become raging, intolerant assholes just because of a new logical twist in their thinking. They will find a way to accommodate the new perspective into their basic character as if it had been there all along.
As for the crusading sort of atheists who feel compelled to badger even the most inoffensive believers, they strike me as the spiritual descendants of Frederick Taylor. In their case, they're obsessed with eliminating intellectual inefficiency, even if it results in diminishing returns or outright counter-productiveness. Just imagine how much more we could accomplish if only all these valuable neurons weren't being wasted on metaphysical fantasies and irrational superstitions! Of course, the idea that the world and all its problems can be reorganized and set right by flawless human reason is a fairy tale, a myth, a fable and a superstitious delusion itself. As a rule, it's best to recognize what "good enough" looks like and stop there.