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.

"And that by chance if an honest man such as yourself should make enemies, then they would become my enemies. And then they would fear you."