My interpretation is that "You" is an alien perspective that the Main Character doesn't understand. Like, I have this totally reasonable belief, and then You show up believing this weird other thing. ...Oh, or like that. When I think "You," I think "the Other." I am the farmboy who wants to escape myself, and You are the Other, the last sensei of a mysterious art, who promises to unlock my potential if I Trust him.
So I suppose the answer to your question would be the first one--it's the Main Character saying You to their opposite--but perhaps my explanation sheds a little more light on it.
(EDIT: When I think of You, I think of it as being said like this. )