People often use the phrasal verb "believe in" when they ask you questions about gods or certain scientific theories. I think this phrase causes a lot of confusion and misunderstanding. It's probably best to avoid using it.
Off the top of my head I can think of three meanings for “I believe in X”. (Later while browsing at a bookstore I checked a big fat unabridged dictionary and my initial guesses below proved to be mostly correct.) Here they are:
1. I think X exists.
2. I have a trust or confidence in X. (eg. I believe in America! Of course the person isn’t saying America exists, or I believe in you honey, said to a spouse or child.)
3. I approve of X. (Usually used in the negative. Eg. I don’t believe in watching TV.)
Depending on the meaning intended by someone asking a question using "believe in" quite different answers are appropriate.