"I believe you" is when you believe that something someone is saying is true. "I believe in you" is when you think a person is capable of something- "I believe in your abilities". We use the same construction to say we "believe in" the existence of God. "I believe in God" means you believe God exists, whereas "I believe God" means you believe what God said.

"I believe you" is more of a statement for you believing that someone is telling the truth. "I believe in you" is more of saying you have faith in someone, and you think that they are able to do something.