My wife, despite having been a microbiology major, has gradually become very religious, primarily, I believe, out of the groundless fear that our children will have no moral center without it. She frequently accuses me of using skepticism and science as a religion, and always trots out the old "Science is untrustworthy because it's always changing" saw.
Every night, I read to her until she falls asleep, and we've gone through dozens of books that way over the years. I am currently looking for great books that I can read to her to help show her the beauty of science and skepticism--but they need to be the sorts of books that she won't feel initially threatened by. (So no GOD DELUSION right off.)
I think that if I can read her a number of great books on logic, reason, skepticism, and science, that she'll inevitably have to come round, to some degree.
I just read COSMOS by myself, and I'm thinking Carl Sagan's DEMON-HAUNTED WORLD might be a good first one to read to her. Any other suggestions?