You're misinterpreting Tom's and Sonny's relationship. They were like brothers, such was represented in the flashback scene at the end of GFII between Sonny and Michael when Sonny went after Michael.

Michael reveals his feelings about Tom early in the film. He intriduces Tom to Kay in the course of which he tells her his last name. He then tells Kay that Tom is not a Sicilian. Both statements are accurate, but they are also indicative of Michael's lack of comfort with Tom.