It would seem like, in general, religion and Faith (with a capital 'F') isn't really depicted very well in Science Fiction and Fantasy. Most books (e.g. Dragonlance) tend to get it wrong, and I think the reason is that in Reality there is very little certainly about what's actually really going on. There are many viewpoints and interpretations of the same real-world events. A very tragic event to some, may be God's retribution for mankind's sins to others, or it may be karmic repercussions of a world full of hatred, or it might be an insidious global conspiracy, or any number of other things. Faith and Religion gives us the room to understand, give our personal interpretations to these events, and come to terms with them.
But the entire point of Sci-fi and Fantasy is exactly the opposite: The whole idea is to provide an escapist alternate reality, a reality that's completely different than ours, which the author has to construct and spoon-feed us piece-by-piece. Unless the author's very gifted, he/she is not going to have the bandwidth left to talk about different secondary interpretations of that reality. So religion and faith end up having very little "wiggle-room" for interpretation in that universe: The religion is either Wrong or Right in the Canon, and no in-between. Faith is either the blind fanaticism of a zealot, or a vaguely secular humanist "belief" system, or most commonly some mechanics of the universe itself (i.e. divine magic): none of which resemble real-world Faith.
The only book that I've seen get this right is Dan Simmons' Hyperion series. Frank Herbert's Dune series may get this, but I haven't read enough of the series to be able to tell.