I think of it like this:
1) Lebron and Wade attack the rim more than just about anyone in the league, and the celtics are a jump shooting team. Against the heat, until Paul Pierce and Ray Allen start playing like its 2006, and rondo attacks the rim consistently like he did tonight, we're always gonna have a free thrown discrepancy.
2) superstars get calls. Lebron and Wade are two of the games biggest.
3) refs are human, and screw up calls, often in favor of the home team and superduperstars. The heat had both tonight.
I believe my 3 reasons, because believing the alternative (that there is a concerted effort on behalf of the league for the heat), just makes it unfun to watch.