For me, religion in fanfic has to be dealt with carefully. It has to be in character, to suit the character. I can think of some characters where not mentioning their religion or having them expressing religious beliefs opposite to those they have on the show is a problem. For example, Booth is Catholic. Although we don't see a lot of his religion on the show (or didn't when I watched - I'm waiting for the DVDs to see most of season 2 because my reception of FOX is awful), it is shown to be a pretty big part of him. So the respect in churches, respect towards prayer, and freaking out at Jesus being compared to zombies is to be expected, and needs to be remembered when writing fic. (On a side note here, I was very impressed with how the character was done. It was nice to see a character that plainly had some strong religious beliefs, but was not defined wholly by them, did not feel the need to bring it up every episode, etc.)
OTOH, most characters on tv today are not affiliated with any religion. Secular celebrations of Christmas is the most you get for most of them. So giving them any strong religious belief seems OOC in fic.
For Superman, I think it's more difficult to give him a religious affiliation, even in AU fic (where you don't have to worry about OOCness). I think this is because Superman is representative of the masses, is a symbol to us all, is there to serve us all, etc. And when you give him a (strong) religious affiliation, you almost slice that segment down. He becomes representative of or symbolic to that group rather than the whole world. It narrows his focus from humanity to a segment of humanity. Probably wouldn't be an issue if he were not-deeply-religious Muslim/Catholic/etc. (really wouldn't make his behaviors much different than they are on the show), but certainly would be if he was a religious official of any religion or was an extremely religious person, IMO.
