I'm an atheist and did not feel like the show was pandering to Christians. Ron Moore himself has said he's not a believer so the idea that the show was trying to put out a Christian point of view doesn't really hold up, especially when you consider the "God" of the show isn't particularly moral.
As for the likeability of the characters, I don't know what to tell you. I've never understood why people have to like the characters to enjoy a show. It's about whether they're engaging, not whether or not you'd want to hang out with them.