It's very easy to sympathize with underdogs. It's clear that there's some cultural/social tension between the extroverted and fun-loving and the quiet and wallflowery--or the pagan and the monotheistic. (Reed kind of equates the two, but I think that one sort can exist without the other.) I think that the blame for this social tension lies, in our minds, with whoever is in charge; whoever has had the opportunity to do the most harm to the other side. In Mumbo, Jes Grew is, for the most part, the underdog, and the Atonists are "the powers that be" (Mr. Mitchell's words). I think this has been true for most of history as well: monotheism and western culture have, for whatever reason(s) (guns, germs, steel, and perhaps, if Reed is right, a desire to dominate) come out on top, and done extremely reprehensible things with this privilege.
But to middle-school-Natalie, Atonism was most certainly the underdog. I think that I wasn't alone in this perception. The word "wallflower" doesn't tend to evoke evil and controlling. It usually means quiet, nerdy, too awkward to dance: underdog. I know it's hard to believe, but some people actually do find it fun to discuss snobbish things like, "if I stand in the water today am I the same person who stood there yesterday etc. etc."(Although I think it's usually the river that's not the same...is that the thought experiment Reed's referring to?) Unlike Moses's privileged, over-dog mom, these kids are generally not in a position of power in middle school.
Sympathy for the nerds, and blame on the socially dominant kids is a common theme in popular culture, especially in movies and tv shows centered around high school (Mean Girls, Freaks and Geeks, Perks of Being a Wallflower). There are very important aspects of the Jes Grew-Atonist dynamic which barely carry over at all in these stories, like the stuff relating to race and religion. However, there are certainly some parallels that would suggest that, by sympathizing with the nerds, they're being told from the Atonist point of view. Set is unhappy because he can't dance and no one likes him. Presented this way, he sounds like the homely but lovable main character of a quirky coming of age novel. You just have to ignore the murder and oppression and cannibalism.
Though I think Reed's metanarrative is a very useful one, taking the wallflower perspective doesn't rob these movies of their merit. I think that Atonism looks bad when it's in control, and Jes Grew looks bad (though objectively much less bad) when it's in control. Having fun is great, but quiet thoughtfulness is not objectively amoral.
Coming out of an elementary school with a relatively introverted (and fairly white) student body, and entering a huge middle school full of Jes Grew was sort of terrifying. People were so confident, and they listened to all this unfamiliar music, and were so open with sexuality (I mean, by a goodie-goodie sixth grader's standards). Most of them were totally friendly to me, but life was not so fun as a wallflower, and in my mind that was in part because of them--the "cool kids". I put (past tense) some blame on Jes Grewish things (like popular music) for my discomfort in middle school. I have to admit that I was a little bit of an Atonist--not explicitly racist, but also not understanding of cultural things with African American roots, like hip hop. Uni has helped me develop more of an appreciation for these things and realize the errors of my past beliefs (though I still can't dance).
An unimportant sidenote: I love that Freud's comment about America being a big mistake made it into both Mumbo Jumbo and Ragtime.