This analogy...makes a great deal of sense if you believe that the idea of God is an absurdity dreamed up by crafty clerics in darkest antiquity and subsequently imposed on the human mind by force and fear, and that it only survives for want of brave souls willing to note how inherently absurd the whole thing is...[t]he story of our civilization, in particular, is a story in which an extremely large circle of non-insane human beings have perceived themselves to be experiencing an interaction with a being who seems recognizable as the Judeo-Christian God, rather than merely being taught about Him in Sunday School. I am unaware of anything similar holding true for orbiting pots or flying noodle beasts. And without the persistence of this perceived interaction (and beneath it, the intuitive belief in some kind of God), it's difficult to imagine religious belief playing anything like the role it does in human affairs, no matter how many ancient scriptures there were propping the whole thing up.I don't find this persuasive at all (full disclosure: I do not consider myself to be an atheist). So because societies throughout history have perceived that there is a God, and they've written stories about his greatness, that in and of itself legitimizes God's existence, thus atheism should be rejected out of hand? No, not so much.
Societies have told lots of stories throughout history that have turned out not to be true. For generations the story of the Dutch boy who put his thumb in a dyke to save his town has been told. Turns out that's not true. People love to tell the story of George Washington cutting down the cherry tree - that's been going on for close to 200 years. Not true. Heck, the story of Rickey Henderson not remembering that John Olerud was his teammate on another team is spectacularly hilarious. Alas, though it is more recent, it's not true either. But, by Douthat's reasoning, if they're told by enough people for long enough, they should be believed, or at least the burden lies with those seeking to disprove the stories, rather than the believers.
Obviously this is an over-simplification of the argument he's making. But the fact is that there have been non-believers as long as there have been believers. Just because there has never been a common organization that united atheists (which would kind of go against the whole non-belief in some greater being) should not devalue their opinions in the least.
Put it this way; if 95% of the people in the world say that the say is green, it should not incumbent on the 5% to prove that it's blue. Somehow though, when it comes to religion, that seems to be the case.