You make some valid points, but I think the key to the situation lies in the differences between the Black Plague and Fallout's nuclear apocalypse. The plague could subjectively be argued to be one of the most damaging cataclysms in history, but it left the society and the actual, physical areas it struck (if not their populations) largely intact. Losing a total war tends to have more drastic effects. Fallout's America has been completely torn down, its culture largely obliterated, and historically speaking there are at least as many cases of decimated cultures going extinct or receding to the fringes of society as of those cultures concentrating and fortifying under the strain. The in-game evidence points to pre-war religions falling mostly into the former category. A rare few, in scattered pockets, were reenforced, but mostly, believers are scarce and infervent, probably eclipsed in numbers and orthodoxy by post-war cults and tribal religions (which even still are still a minority of the population.)
Also, Fallout's wasteland differs from most other case studies not only in that the decimation wrought there was near-total, but that the society it was wrought upon was falling from a far loftier height of sophistication. During the plague, people turned to religion in droves out of desperate hope. In the pre-wasteland world, though, people had been taught that science was their hope, and it was that very hope that visited an unprecedented devastation upon them. For the hardcore religious faithful, it must have seemed a final judgment from which there was no salvation, so it was a real double-whammy: if not God, if not
Science!, what was there to believe in?
The Wasteland is largely a post-hope, post-faith kind of place, and I think that's integral to the bleakness of the setting.