I know, I know and in this point I really can understand him and I love Proto Man for this inner-struggle. This post should not say that I don't like him ;-) Just make me a little bit sad and angry.
I think he is one of the greatest characters in the game and Flynn is doing a great job, working on that character and to make him really special and give him a character-history. He has feelings about Roll and Rock, but I also think he doesn't like to know that he could be wrong. I think in MM4 (?) he is forgiving Light but this scene was really affecting with this sentence "To be my brother" as a new function in life. If that would be in a movie I would cry a lot!