stories addressing losing or finding faith

[neural_girl]

I've been thinking about stories that deal with losing and/or gaining religious faith, and how I view them from my non-religious perspective. I've known for a long time that I object to a character gaining faith during a story if it feels like there's a message that that's the good or right thing in general, and not just for the character. I get really annoyed if I feel like there's subtle (or not so subtle) proselytizing going on. But what I've noticed recently, and find interesting, is that sometimes it feels better to me in the context of a story if a character ends up gaining/regaining faith in God, Fate, or some such higher power than if they lose faith for good. I only feel good about the "gaining faith" type ending when it doesn't feel to me like it's a message about what the author thinks is right, or it's supposed to inspire me to do the same (and not always then). but I'm not particularly sure why I should ever hope for that ending for certain characters, given that I don't believe in God, Fate, or any such higher power - I don't think I ever hope for that to happen outside of stories. huh.
I don't have a problem with gods or faith in fantasy books - sometimes they make for an excellent story. But I would expect that I would treat fiction that much more closely resembles real life to evoke more of my impatience with and lack of understanding of most religion. Maybe it just has something to do with my ideas about what makes a "good" ending in various cases, based just on they way the story and the characters are set up. I don't know.