The quote itself is far more interesting than the fact, which doesn't surprise me in the least. If you don't believe in God, then why would you think believers are "fortunate" for putting their faith in a nonexistent higher being? You wouldn't. Yet Rove, for political reasons, must genuflect to the notion that religious people are morally superior to atheists. The line perfectly encapsulates the condescending and way Republican elites have manipulated religion.
I don't think calling religious believers "fortunate" is the same thing as calling them "morally superior." I've heard plenty of atheists remark that they envy religious people their faith in God, an afterlife, the beneficence of the universe, or what-have-you. This sentiment isn't universal, obviously (see Hitchens himself for a counter-example), but I think it's perfectly reasonable for someone who's convinced that life is a meaningless round of pleasure, pain, and Machiavellian campaigning that ends when you die to feel a little envious of people who believe something slightly more optimistic.