(Full disclosure: me, huge science fiction fan. Fantasy, not so much. But to each their own; and done well, both genres let us change "givens" and ask questions about the world that would otherwise be incomprehensible or incoherent.)
So here's the question, and I'm genuinely curious about this. C.S. Lewis notwithstanding, fantasy novels seem to pre-suppose a universe that does have supernatural forces, but the gods and spirits are not from any pantheon we recognize. Viewing from the outside, I would assume this is troubling to Christians. So to any Christian readers: does it ever strike you as strange that here we're reading about a universe with a different set of deities than our own, and yet it's recognizably similar? This just struck me as curious.
Harry Potter must assume a world without the Christian God, or personification-of-evil guys like this wouldn't be running around loose needing high school kids to fight him. Same for Darth Vader and Sauron. Doesn't this stick out to Christians?
For that matter, the same question applies to Christian science fiction fans, although there at least we're not talking about a universe which assumes that other gods are real. Most science fiction seems set in a universe that is a post-Enlightenment rationally ordered secular place with no room for the supernatural. Does this bother Christians, or do they assume that the Christian god is there in the background of science fiction novels, and just isn't a theme in the book or movie? Even those fictional worlds that arguably have deities don't fit a Christian worldview: Star Wars and Star Trek both contain all-powerful god-like entities or forces but they're either explained in scientific language, or explained in mythical terminology that owes more to New Agey silliness than Christianity.
Christians could turn this around and ask atheist fantasy fans how they can deal with a universe that has supernatural spirits. To some extent I think the answer would be the same: suspension of disbelief, and a recognition that we're reading something we know to be untrue. But such a basically irrational universe as Lord of the Rings could only exist in our imaginations, precisely because those imaginations are limited. If there is magic, if the world is dependent on word and symbol (rather than the other way around) how can we be sure the place would have atoms and gravity? But of course you don't watch Conan and wonder if basic physics would have held up in the bizarre realm of the Hyborian Age; you just watch the ass-kicking.
But often we do read this kind of fiction exactly because we want to see how things would be different: if people lived somewhere they knew ghosts were real, or where wizards or vampires were their own class of society. We read them precisely because we care about the huge differences that fall out of changing something basic. For a Christian, a universe with no God or with different gods would certainly count. So the question might be rephrased: what does a Christian think would be a realistic portrayal of a universe with no God? With a different god or gods? How specifically would things look, what would happen differently, if instead Allah were the real God, or Vishnu and Shiva and Brahma?
Alternative theology is always a fun conversation starter. (Here's an article about a rationalist re-telling of Lord of the Rings.)