Yeah, Rondo's free throw shooting is definitely a weakness. He ranks 360th in the league in FT%, and among players with 20 or more FTAs this year, only Brendan Haywood, Spencer Hawes, and Tracy McGrady are worse.
That said, it's early. His career averages suggest that he's going to get back up to the 62% - 65% range. That's still not great, obviously, but it's a heck of a lot better than 44%.
One of the biggest issues for the team when Rondo struggles from the line is that it leads to Rondo being less aggressive in terms of penetrating. Doc cited this in last year's playoffs, essentially suggesting that Rondo was playing away from contact. That hurts the team, because Rondo is an amazing finisher inside.
As others have said, the poor FT shooting also makes the Celtics more vulnerable at the end of close games. Ideally, it would be Rondo -- rather than Paul or Ray -- handling the ball in close situations, but the team is handcuffed by Rondo's poor FT shooting.
The good news is that Rondo has the capability to be a good FT shooter. He's had long stretches where he was over 70%, which is respectable. If he can get over whatever is psychologically holding him back at the line, I think he'll be fine.