Coyne argues that atheism, or metaphysical naturalism, entails that there is no free will as it is commonly understood. In other words, at every given moment there really is only one possible future and the conviction that we really were free to choose other than what we did choose is an illusion.
Toward the end of his column he talks about the implications of his denial of free will for our belief that we're morally responsible for the choices we make:
But the most important issue is that of moral responsibility. If we can't really choose how we behave, how can we judge people as moral or immoral? Why punish criminals or reward do-gooders? Why hold anyone responsible for their actions if those actions aren't freely chosen?Set aside the objection that, given determinism, there is no "good" or "bad" behavior, just behaviors that we like or don't like. Still, Coyne never addresses the important point. If determinism is true not only are reward and punishment never deserved, but moral outrage is absurd. The man who tortures children and then kills them is not immoral. Those who let others starve while indulging themselves to excess are not immoral. The person who legally bilks the elderly out of their life savings is not immoral. There's no moral duty not to do any of these things.
We should recognize that we already make some allowances for this problem by treating criminals differently if we think their crimes resulted from a reduction in their "choice" by factors like mental illness, diminished capacity, or brain tumors that cause aggression. But in truth those people don't differ in responsibility from the "regular" criminal who shoots someone in a drug war; it's just that the physical events behind their actions are less obvious.
But we should continue to mete out punishments because those are environmental factors that can influence the brains of not only the criminal himself, but of other people as well. Seeing someone put in jail, or being put in jail yourself, can change you in a way that makes it less likely you'll behave badly in the future. Even without free will then, we can still use punishment to deter bad behavior, protect society from criminals, and figure out better ways to rehabilitate them. What is not justified is revenge or retribution — the idea of punishing criminals for making the "wrong choice." And we should continue to reward good behavior, for that changes brains in a way that promotes more good behavior.
None of those things are wrong because to be wrong an act has to be in some sense freely chosen by the agent. If a "choice" is merely the result of fermions and bosons spinning about in someone's brain then there simply is no moral responsibility.
It's understandable why Coyne would finesse this point by raising it and then changing the subject to crime, though. If he were to follow the logic of his claim that we can't hold people morally responsible for their actions most of his readers would be repelled by his conclusion and thus repelled by the atheism that leads to it.