I'm not sure it needs a whole book: a theory is backed by demonstrable fact. When there are facts that do not coincide with the theory, scientists find a new one to match all the acts. Faith, on the other hand requires no facts, just a belief that ones view is correct.
I think the best reference for this, where I picked it up at least, is The Demon Haunted World by Carl Sagan. He investigates all sorts of things like alien encounters, goes into the history, etc. I think this is the book that made it all finally click for me, but it has been some time.