This is a question for everyone, religious or not, vehemently anti-religion or not. How much religion is too much in a story not shelved in the Christian Literature section?

I've often wondered what it is that gets something marketed as "Christian Fiction" as opposed to not. C.S. Lewis gets put both there and in regular fiction for his Narnia series; likewise Madeleine L'Engle's Time Quartet also gets a space in both. Allegorical fantasy, at least, seems to be able to play both sides of the fence. 

Then there are all the Christian romances, which — I must admit — bemuse me just as much as their sexy counterparts, because while they have just as much sexual tension and awkwardness, instead of the inevitable dive into the sheets, we get kisses (maybe) and a lot of conversation. These are definitely religion-only, mostly because I can't imagine the two demographics cross over very much.

But what about books where religion isn't a theme or a plot point, but is still part of the characters' lives?  They obviously don't belong in the Christian Lit section, any more than regular books that include a love story belong on the Romance shelves.  So as such, is there a limit to how much religion can play a part in a character before mainstream readers (or agents, or editors) start shutting off?

It's a real problem, I think, that religion rarely comes into stories as anything but negative — whether it's the amusingly sheltered Flanders family, the intolerant orthodox parents of a gay teen, the sexually-repressed religious school that hampers our free-thinking heroine, or the bitter, reactionary Hollywood Atheist (because few atheists are happy in fiction). Because of this, mentioning someone's religion — or lack thereof — in a story brings with it a lot of baggage.

I am Christian myself, and openly so; my characters range from anywhere along the Judeo-Christian belief spectrum to complete atheists.  I don't write Muslims because I don't know enough about the beliefs to do a good job, but if a character insisted, I'd have to do research and talk to people to find out. Sometimes I wonder if this religious content will give me trouble later on.

The thing is, my Christian characters aren't perfect — they mess up, they lie, they make mistakes, they hurt people, they have premarital sex (some of them). And when they do, while it's not applauded, and while they do their best to make things up, there's not a moral behind it. I don't write parables. On the other hand, they do attempt to be good people, and their beliefs do influence their lives. They attribute part of their happiness and their selves to their religion. Many of them are gay or bisexual; some take a while to conflate the two, others never saw a problem. None of them have homophobic religious parents. There are enough negative portrayals of religious characters that I refuse to write them, ever.

I'm writing a collaborative YA urban fantasy series with a Jewish main protagonist; when he's younger, Judaism is mostly something he does because that's the culture around him, but the older he gets, the more real his faith becomes to him. There's a huge plot element that results in a breakdown, and part of it is a crisis of faith resulting from said plot element. 

Meanwhile, I have atheists and agnostics; some apathetic, some militant, but all of them are good people. None of them are morally corrupt or bankrupt; none of them cry themselves to sleep from the emptiness of it all, or drink or take drugs or dive into promiscuity to fill the hole. Some have their reasons for not believing; others have just never been given a reason to believe. Some desperately want to believe, but never find themselves convinced, no matter how much they may want to. Some think it's stupid. Some just don't care. Some convert; some don't.

Would any of this turn people off?

I ask not because I intend to 'sanitize' my work of religion, nor will I apologize for it (it's as much a part of those characters as atheism is to the others), but because I'm honestly curious. I know people who will put a book back if a character mentions God in a positive way at all; is this a general trend? Is there a point where you would stop reading because of religion, and if so, where is that line?