I have a very different opinion on the Vito-Tom-Michael relationship than most of the people on this board.First of all I think Vito made a good bargain by taking in Tom as he was smart but he was not doing it on purpose. Tom could have chosen any other line of work but he wanted to be part of the organization. He rose pretty high too so I do not think his loyalty and skills went unhonored or unnoticed. In the book he seems to be fully aware of his situation and very satisfied with it.

Secondly, I think that Michael and Tom had a closer relationship than the majority opinion here. Tom was the only one who understood Michael and he knew this(even if Tom did not like everything Michael did).I think even Michael had to have someone like that around. For me the funeral scene in the book and the movie tells the same- Tom understands everything and supports Michael.

Also I always thought that in Godfather II when Michael yells at Tom is to tell him what is going to happen (with Frankie and Fredo too) and asking him whether he will go along with that. This was not a happy conversation but I see the tension at a different place than most people. And Tom says yes, and goes to deal with Frankie personally.

From Puzo's screenplay for Godfather III that was never made because of Robert Duvall it seems that old Michael and old Tom are in a brotherly relationship. Of course this does not mean that they always had a perfect relationship as with real brothers.