I could never put my finger on it, but for some reason, Mike resents Tom. I have a feeling that maybe he felt the Don was giving Tom too much power over him (mike) and that he should have the right to do what he wants. I get this form the flashback in 2 where mike questions tom "You talked about MY future?" I think that's why that scene was brought in.
Michael and Tom are both very intelligent. Sonny can work with Tom, because Tom could play the egghead while Sonny supplied the personal force. Michael and Tom don't complement each other in that way, so if they tried to work together Tom would wither and become resentful and possibly a threat.
