I think Sonny did regard Tom as his brother, but he said two stupid things that may have shown resentment: When Tom advised him to make the deal with Sol if Vito died, Sonny said, "It's easy for you to say, he's not your father." Later, before dinner, Sonny shouted at him, "Pop had Genco, look what I got." But Tom was Sonny's choice for brother, not Michael's. Despite his introducing Tom to Kay at the wedding as "My brother Tom Hagen," and calling him brother after the Tahoe shooting, I don't think Michael ever loved him as a brother the way Sonny did, and he probably did resent Tom--certainly he did in that flashback scene at the end of II.