Tom's Donship has no bearing on any of the plot to follow. It only serves to give Michael the opportunity to tell Tom he always thought of him as a brother.
Exactly, MC. The Tahoe shooting made Michael realize that Tom, who he'd shunted aside and abused, was the only person he could trust at that point. And he needed Tom to manage things while he was gone. So he tried to make "amends" by crapping him up to a fare-the-well: "I kept things from you because I love you and respect you"; "you're my brother"; "you're gonna be the Don." It was all B.S., as we saw--as soon as Michael got back from Cuba (after finally finding out who the traitor was), he was back to being abusive toward Tom.
