Yep. The good guys are religious, but we learn that the source of their religious belief is based largely off the drug induced mind expansion of genetically special “prophet”, the manipulating folk tales of the Bene Gesseret, and even human nature’s miraculous ability to adapt to seemingly unhabitable environments. I saw religion portrayed as a tool used to satisfy a sense of monarchistic duty. Kind of a morally beneficial lie.
Dune is actually very “Survival of the Fittest”.

Yeah, but that’s sort of in the Gospels, too.

I think Robert Jordan’s Wheel of Time series counts. While everyone doesn’t have the same religious beliefs, there are religious beliefs of a sort there. If you think of supporting the Aes Sedai as a religion.

Also, Ursula Le Guin’s Earthsea series.

Of course, there is also a fight (in both novels) against “the establishment that has been corrupted” (I’m grossly over-simplifying here).

I agree with BSG, of course. Although the relationship with religion is very complicated.

I’ll keep thinking about this, but I think there are more than what one might think of easily.

Maybe I’ll hold with my perception that he’s the only truly bad guy. ;)

Good guys and bad guys (Human and Cylon) are both religious in that series and perhaps the only true bad guy is an atheistic scientist.

Have you read the second book and beyond? Have you even understood the underlying themes of the first? I suppose at a superficial level “Dune” qualifies, but the hero uses religion to minipulate the masses. Religion is just a tool to keep civilization from stagnation. The more the series continues the more this becomes evident. The true power in these books isn’t religion or technology, but spice.