Thats a good point. It just seems as if throughout 1 and 2 that Michael resents Tom. Michael holding Tom somewhat responsible for Sonny's death and him not being Sicilian explains that. However, I do agree with the earlier post that Michael wanted to keep Tom out of the illegal aspects of the family business as an eventual avenue for going legitimate someday and as a way of keeping Tom completely trustworthy, like when he makes Tom Don during his visit to Cuba.
But why does Michael have Al Neri dig up dirt on Tom and then Michael agressively asks Tom (during their meeting when he mentions Tom's mistress) if he is leaving the family business or going to go along with the things that he has to do? Tom asks hom why he hurts him like that? Is it simply because of Michael still holding him responsible for Sonny's death or something else?