I never thought that there was a relationship between the two men. Kraft is all about image/brand and wants the Pats not only to be America's team, but the world's team. Belichick just didn't give a crap and almost relished in being an a-hole and hated across the league. Kraft must have steamed every time a Belichick news conference got really contentious.
As for Belichick and Brady and other players, it has been reported that Belichick's relationship with players are one way when they are on the team and another when they leave. When they are on the Patriots, it is a cold relationship and they rarely see the human side of Bill. Afterwards, Belichick is a completely different person - personable and funny.