I think that there’s a lot to what Vinnie has said about Bobby not making his bones until he was a Captain, but I think that has more to do with Tony than with Bobby. Tony assigned the kill to Bobby as punishment. I think that Tony viewed Bobby as a good, faithful man, someone who valued family and authority as well as a person who wasn’t afraid to love his wife and kids. Tony also valued those things, but in the eyes of Tony’s world, those values made a man weak, and I believe that Tony viewed Bobby as the “weaker” side of himself.

Bobby was known as someone who never had a piece on the side, had interests outside of his world, and had never taken a life. Tony admired that kind of person in theory, but Bobby was perceived as weak, and Tony could never be perceived as that.

Think about the high school bully who is constantly beating up the kids he calls “homos,” and what’s going on in his mind.