Thanks, Klydon.
Tom was Vito's choice for consigliere after Genco died, not Michael's--hyper-controller that he was, only Michael could have been Michael's consigliere.
I believe, though I can't prove, that Michael may have blamed Tom for Sonny's demise. A real Sicilian consigliere would have foreseen that Carlo's public beating and humiliation by Sonny would lead to revenge. Yes, Tom tried to stop Sonny and sent men after him, but Michael may have figured that a real Sicilian consigliere wouldn't have let it get that far in the first place.
As Klydon said, Tom really blew it by not knowing about Pentangeli's survival and that Questadt "belongs to Roth." Tom told Michael that "our people with the New York detectives said [Frankie] was half-dead, scared, talking out loud about how you betrayed him..." DUH-H-H, Tom: where were you and your people with the New York detectives when you counseled your one and only client, Michael to perjure himself five times?
In the novel, following Sonny's murder, Tom himself realizes that he's not a wartime consigliere..."old Genco would have smelled a rat."