Pickles, I'm coming late to this, but I'll share some scattered thoughts.
First, for context, I'm a believing, active Christian, raised (baptized and confirmed) Lutheran (LCA) (waves hello), involved with InterVarsity, a fairly conservative college group, attended an American Baptist Church for a few years, then Episcopal, and now I'm Roman Catholic. I don't believe in not reading books because of content, or advising others to do so, but I understand where some very conservative folks are coming from.
I love well-written fantasy. One of the many reasons I love fantasy is that it often takes me out of this world to see things in a different light. Some of my favorite fantasy gives me a glimpse of heaven, or more like a feeling of it. LOTR and Narnia would be high on that list. In Lewis' nonfiction, he talks about this - that the Christian story is like your favorite story, except it's true. The 3rd LOTR movie inserted an extra scene, where Gandalf is talking to Pippin, telling him about the far country, and I think it fits with the underlying premise, tone, feeling, of the books. They have an underlying world-view that is consistent with Christianity.
That's one of the things I look for, the worldview. Pullman's trilogy does not have this. In fact, he's openly antagonistic to Christianity, and even though I love the books in some ways, and let my then-9-yo read them (and we discussed them), they just make me spitting mad to read, so I don't re-read them, as I normally would a favorite book.
Books that are set in this world are much more problematic when it comes to dealing with fantasy/Christianity. Harry Potter skirts the issue entirely. Christmas is there, but it's entirely secular. I'm okay with that. But really HP has an underlying worldview that is consistent with Christianity, which is why MOST Christians are fine with them. There is good and evil. People have to decide which side they're on. There is Truth. HP is in no way a relativistic - i.e., current secular thinking - book; she sets her worldview as being opposed to Voldemort's (which is straight out of Nietzsche, where he says something in Book 1 like - there is no good or evil, only power and those who aren't afraid to use it). The "witchcraft" in HP bothers me not one whit; it doesn't even feel like witchcraft. In the context of the book, it certainly is not evil or anywhere allied with that; it is simply a tool.
I get bugged when a fantasy that is set in this world, or partly so, references Christianity in a dismissive way (or worse). Pullman's among the worst. Susan Cooper's series is mostly fine with me, but in one place she mentions a priest who is clueless about the real powers in this world, or something like that. Fly By Night, which I like very much for various reasons, is also, in places, dismissive of faith in general (I started a thread on that if you want to see more of my thoughts there). Even A Wrinkle in Time, which I love for lots of reasons - and I like other stuff by L'Engle, irritates me a bit because at one point she places Jesus as equivalent to other thinkers.
One recent book that I think handles this whole question very well is Wizard Heir by Cinda Chima. She has all kinds of magic elements, wizards, etc. placed in this world. She mostly sidesteps the religion question, but she does a couple of things I like. She mentions religion 4 times (I think). She mentions that the mc, Seph attended mass with his foster mother growing up (who is seen as a good person). The foster mother is devout, but won't let the priest do an exorcism when things happen around Seph that are, um, strange. It mentions the mc finding comfort in Latin masses. It has a brief exchange between 2 characters, where it states clearly that the whole wizard thing is NOT a religion, and it's compatible with Catholocism or other religions. And at the very end, it mentions the mc and others attending Christmas Mass. So she just very subtlely injects a neutral to positive view of religion and makes it clear that the magic in the book isn't religion, and is not a substitute for it. Simple.
On a different note, I agree with Jen that there are all kinds of stuff I would read, but not necessarily that I would write. I think as writers we have to tell the truth. That's a tricky statement. How do you write a book set in this world, that involves fantasy elements, which by their nature deal with the nature of reality, truth, things not seen, etc. and not deal with religion? If you're a person of faith, that is. I love, love, love HP, but I don't think I could refer to Christmas in a completely secular way, because that's denying truth. On the other hand, I'm not trying to write a Christian fantasy.