What bothers me most about the use of religion in comic books boils down the the function that it actually serves. All too often, religion is used for one of two purposes:
1- As a shortcut to characterization.
2- To fulfill a writer/artists interests or their perception of their reader's awareness.
There's nothing new about using religion as a characterization shortcut. Daredevil needs to be Catholic because Catholics are wracked with perpetual guilt. Right? Well, no. Their portrayal leans in that direction in media. Other times, though, you end up with portrayals that are so completely opposite of the stereotype that they stand out rather blatantly. Monet, for example.
I think my favorite portrayal of a religious character in comics comes from the short-lived Streets of Gotham series; issues 5 and 6. An invisible villain tries to goad a priest into killing Huntress and Man-Bat by pretending to be the voice of an angel. I initially thought this was going to be a religious-people-are-crazy type storyline, but was pleasantly surprised in the end when the priest stalls long enough to zero in on the villain's position and then clubs him with a shotgun.