I'm going to re-answer your question with, hopefully, a less pathetic answer than the one I originally provided.
Recently, I decided it was time to work on my writing style and therefore sought out modern fantasy masterpieces to aspire towards and enjoy. Now do know before I continue that I'm a Christian. If you'd like the specifics, I'm Pentecostal though I prefer not to associate with any one denomination as I don't really believe in the concept of denominations. But that's for another day.
Anyway, Harry Potter was the first series to come to mind. The movies have been completed for almost four years but people are still talking about it altogether. Naturally, I decided that since I'd heard so many good things about J.K Rowling as she develops her writing throughout the series I thought it would be an excellent idea to sit down and read all seven books. I mean, I'm developing my writing or seeking out to do it, and i love imagination, so it's a perfect fit.
Before I started reading Harry Potter, my mother was all for my writing dreams. I want to write secular fantasy books (and she knew it), and I've been slowly developing several series that take place in the same world and simultaneously work together to overcome one evil. Anyway, I'm about three or four books in. One day I'm in the car and my mother says, and I quote, "I wish you'd use your talents for God."
She's never said anything like that before. Not until after I started reading Harry Potter (I'll probably mention that if she says it again. I'm like that. I address things bluntly and head on to get any conflict out of the way).
I think Christianity connects fantasy with anti-God. Back when a lot of culture was Christian based, dragons and witchcraft became the prime target for being casted as the evil in the story. It's where today's stereotypes come from. If you think about it, that makes a small portion, therefore it's being generalized as bad. But, that's also something the world is doing today. Focusing and generalizing one section of something and coming up with a faulty conclusion. Look at the conflicts in the Middle East. Because of that, a lot of people are generalizing a new negative stereotype against Muslims. It's, of course, false.
However (please no one take offense) I believe that generalizing is the wrong way to approach this. Because all good can have some bad, and all bad can possibly have good. While people believe that fantasy are very anti-God, that doesn't mean they are anti-God. In addition, it's just a book! It doesn't reflect reality, or make some massive statement about being anti-God. It reflects one writer's imagination, and the world they've put together.
When it comes to writing, every writer has, most likely, ticked off many readers or offended others. Never be afraid to write what you're passionate about. If people have issue with it, it's their problem. I'm writing with a protagonist that has chestnut skin. People are going to call me racist because of my character's skin colour, but i don't care (we need more multi-cultural protagonist's) because what I have to say is more important.
This is all opinion. Do know that if anyone decides to argue me, I suck at arguing, so i probably won't answer...or I'll wait a bit so I can come up with a good counter argument...hopefully.