He's nasty, but he's not taking over games, and not the most dominant player in the league.
If you can't hit your free throws (especially when it counts like Shaq does) then you can't "take over" a game or "dominate".
I think it would be much more accurate to say that he's dominating the paint, which he certainly is.
The problem is that if the game is close, it is in the opposing teams' best interest to foul Howard and put the pressure on him at the line (where he shoots less than 60%).