It is amazing how Michael manipulated Tom, isn't it? It was quite yo-yo like. The scene with Michael right after the attempted hit is amazing. Michael goes on and on about how Tom is the only one he trusts, that he loves him like a brother, etc. When Tom says that he always wanted Michael to think of him that way, he is almost weeping with gratitude for Michael's affection. After having to break the news to him about Kay's "miscarriage", Tom is definitely on the outs (killing the messenger for sure), but Tom has toughened up somewhat by the end. When Michael tries to humiliate him with the mistress remark, Tom outright asks him "Why do you hurt me, Michael?". I think he's wising up to Michael's ways at that point.