I am repeating myself here, but it is clear thatSonny and Tom had a much closer relationship than Tom and Michael. Sonny and Tom both knew each other's shortcomings and their strengths, and they were really more like brothers. While Michael was in his rebellion period and then fighting in WWII, Tom and Sonny were learning the family business at Vito Corloene's knee. Vito also had great affection for Tom. If you look at the dynamic Tom and
Sonny often raised their voices to one another when they got angry.

On the other hand you never see Tom get angry with Michael. He gets hurt, but never angry, and likewise Michael shows little emotion toward Tom unles it suits some ulterior motive of Michael's.

So when Tom yells at Sonny that he's getting quite a reputation as a hot head who is screwing up business, Sonny retorts by saying Pop had Genco, look what I got. Immediately Sonny apologizes and puts his arm around Tom and they go off to dinner.

When Michael wants to tell Tom his shortcomings as a wartime consigliere, he tells him just that in a measured, cold tone, and when Tom, hurt by the comment says "maybe I could help." Mike says "You're out." Sonny would have never spoken to Tom that way, nor would Vito. In fact in that scene Vito tries to save Tom's hurt feelings by saying he never thought he was a bad consigliere, but that his own son was a bad Don.

Even the little things show this distance. As was pointed out in this thread when Mike introduce Tom to Kay he goes through this whole thing about how he is not a Sicilian etc. Notice the scene when Michael leaves the house to go on his mission to kill Sollozzo and McCluskey, and knows he will be gone for a long time, he gives Sonny a huge bear hug, but when he says goodbye to Tom he just puts his hand around the back of his neck.