Good point about Tom. Michael was in the room after Vito was gunned down and all the guys were talking. He heard Tom tell Sonny, "if we lose the old man, you make the deal." Michael's distrust of Tom likely got it's origin in this very meeting, because of that line of advice. As a result, Michael witnessed first-hand Tom's inability to be a wartime consigliere, i.e., not going against the Don's wishes, no matter what the situation is, like Genco would have done. That's why Michael excluded Tom later on, and said so confidently, "you're not a wartime consigliere." Also, if you notice, Vito tells Tom that he has all of his confidence, but never mentions him having his TRUST. I'd bet dollars to donuts that Michael told Vito in private of Tom's advice to Sonny the day Vito nearly died.