Maybe Michael never got over Sonny dying and blamed Tom alot. That may explain why Michael was so horrible to Tom.
That does explain why Mike was so horrible to Tom. Again, everyone in Michael's life, at least at that point, were utilitarian to him.
But Tom was little different. He sanctioned and facilitated murder and mayhem, the destruction of people and institutions, and was quite willing to participate in the rending of the societal fabric.
