It has to do with choosing either Pierce or Rondo. Both players need to dominate the ball to really be effective. Pierce played really well in game 4 and although Rondo put up the points that game, you could see the effect on him with him ending up with just 3 assists. In game 5, both his points and assists were effected.
What happens when Pierce has it going is we usually run an isolation plays for Pierce. Then Pierce does his thing and he either takes a shot or passes it off with less then 10 seconds left on the shot clock. What happened last night is Rondo's defender double teamed Pierce so Pierce had to pass to Rondo with the shot clock running down and Rondo had to either take a jumpshot or try to find somebody open quick which is playing to his weaknesses. Rondo is forced to be the finisher instead of the creator.
On the other hand, earlier in the playoffs when Rondo had it going he was the one dominating the ball and Pierce was struggling. Rondo was penetrating the defense and kicking to Pierce for open jumpshots...but Pierce isn't really comfortable with that game. He likes to isolate and take shots off the dribble. Also, I think Ray Allen is somewhat dependent on Rondo playing well so Allen's struggles have a lot to do with Rondo not playing as well as in the Chicago series. So it's a tough decision between your best players/most explosive offensive player or your pg/sg. Pierce has it going right now so you have to keep going to him.