The Only Two Good Arguments for Atheism" where in it, he criticizes atheism, by arguing that the New Atheists have no good arguments. Bare in mind now that New Atheism doesn't equal atheism. So whatever flaws the New Atheists have made in their reasoning or arguments doesn't necessarily say anything about atheism simpliciter. I've even said over and over that the New Atheists have not made the sharpest arguments for atheism.
But this piece is just terrible. As someone who's studied atheism, religion, philosophy, science, and the arguments in the god debate, it's so easy for me to spot ridiculous criticisms of atheism. Some people can fall for this stuff. I can't see why. I guess they're preaching to the choir mostly. I decided to leave a comment — just some quick thoughts on how wrong the piece is. I've included them below.
All the New Atheist need do is hope that his reader won't inquire too deeply into just how he arrives at certitude about what "good" or "evil" is without smuggling in all sorts of transcendent categories from a supernatural worldview.
Quite the opposite. All the New Atheist needs to do is inquire deeply into just how the theist arrives at certitude about what "good" or "evil" is without smuggling in all sorts of consequential and deontological categories. Most theists cannot even define what they mean by "goodness." They will see that if they use anything having to do with secular morality to define this (consequentialism, deontology, virtue ethics) they will be saying goodness is a secular concept. And making a circular argument that God is goodness and goodness is God obviously is a non-starter.
The problem is this: Trying to derive a moral universe -- any moral universe at all -- of Should from a purely materialistic universe of Is turns out to be impossible. The perfectly just outrage of a Hitchens at some crime by a theist turns out -- if you grant the New Atheists' materialism -- to be just one more biochemical reaction. And privileging a biochemical reaction merely because it is a lot more complex than, say, combustion is as crude a mystification as bowing down to a rock because it's really really big.
That "crime" by a theist that Hitchens was often pointing out was a mandated religious prescription, like circumcision, the subjugation of women, or the discrimination and/or killing of homosexuals, apostates, or atheists. So what do we do when just outrage conflicts with religious law and custom? Or is Hitchens's outrage in these situations not just? What determines what is just and what isn't? Citing a religious holy book like the Bible is going to open up problems for the theist.
Put briefly, you propose a huge metaphysical hypothesis that Absolutely Everything popped into existence 13 billion years ago with the help of Nobody, but loaves and fishes cannot pop into existence 2,000 years ago with the help of Jesus of Nazareth, despite the eyewitnesses who inexplicably chose to die in torments proclaiming He did. The trick to establishing this hypothesis as dogma -- when the odds currently stand at 10^137 to 1 against the fine tuning of the universe -- is to take a particular methodology that, by its nature, only looks at time, space, matter, and energy and have thousands of people repeat "Only what our methodology can measure is real!" for two centuries over millions of loudspeakers. Voila!
Thinking the world popped into existence out of nothing is not required for the atheist. In fact, science tells us the universe is eternal in what we call a block universe from special relativity. It didn't "pop" into existence because it always existed. And scientism is not required either. Logic can tell us that there is no time before spacetime, so the universe didn't "come from" nothing—as if nothing is a place where things can come from. Simply put, there is a first moment to the universe and nothing before it just like there is nothing north of the north pole. Or, the universe (or multiverse) can have an infinite past. No handwaving is required for a multiverse. It is implied by scientific hypothesis and theories - that's where the evidence is.
There are certainly more than two good arguments for atheism. There are plenty. Consider this bibliography on arguments for atheism from Secular Outpost. And consider some of the arguments I made in my post Why I'm an Atheist.