If I were to suggest that between the Earth and Mars there is a china teapot revolving about the sun in an elliptical orbit, nobody would be able to disprove my assertion provided I were careful to add that the teapot is too small to be revealed even by our most powerful telescopes. But if I were to go on to say that, since my assertion cannot be disproved, it is intolerable presumption on the part of human reason to doubt it, I should rightly be thought to be talking nonsense. If, however, the existence of such a teapot were affirmed in ancient books, taught as the sacred truth every Sunday, and instilled into the minds of children at school, hesitation to believe in its existence would become a mark of eccentricity and entitle the doubter to the attentions of the psychiatrist in an enlightened age or of the Inquisitor in an earlier time.
Then Douthat's dismissal:
This analogy - like its modern descendant, the Flying Spaghetti Monster - 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. As you might expect, I see the genesis of religion rather differently: An intuitive belief in some sort of presiding Agent seems to be an extremely common, albeit hardly universal, feature of human nature; this intuition has intersected, historically, with an enormous amount of subjective religious experience; and this intersection (along with, yes, the force of custom and tradition) has produced and sustained the religious traditions that seem to Richard Dawkins and company like so much teapot-worship.
Douthat's argument is that there is no fair comparison between a native arising of a perception of the divine, and a concocted fable; the point he misses, that Russell and other's were trying to make, is that there is no perceivable difference between a religion founded on a spontaneous eruption of feeling, and a fable concocted by a philosopher. The problem that many atheists have with religion, and those who practice it, is not that anyone believes generally in some divine power; it's that around those "faint tremors" people have over time concocted the most absurd of fairy tales to support their suppression of dissimilar thought, and persecution of those who do not believe similarly.
Yes, many atheists probably feel the "faint tremors" of belief from time to time, but to most of us this hardly seems cause to start denouncing the validity of everyone else's tremors and demanding that the power of the state be bent to our moral precepts. In other words, we atheist would probably take the religious beliefs of people like Douthat more seriously, if people like Douthat would take them less so.