The opposing defenses are focusing on stopping him more now so he is simply not going to get to the hoop as easily. This combined with the fact that he may be subconsciously a little less reckless in going to the hoop due to the injury and also just being a little older in general. The coach/team may also be asking him not to go crazy because they want him healthy for the whole year.
I think Roy H said it well. Rondo is a polarizing player because he has such extreme abilities and extreme weaknesses. He is very unique in that regard. He has also been in the discussion of league MVP and max contracts so he is held to a pretty high (perhaps unfair) standard.
Agree with Roy. I posted something the other day along the lines of Rondo being either first or last in most major categories among PGs - e.g., first in REB and AST, last in FG% and FT%. He's just a peculiar player and therefore not easily comparable to others., So, opinions will be diverse.
On the FGs-at-the-rim point, I would guess that some of it has to do with age (many players take it to the hole less often as they age). But another factor might be that Rondo has fewer offensive threats around him, so his drive-and-dish threat is reduced. If he doesn't have Ray Allen in the corner, he's going to get covered more tightly on drives, and therefore do that less often. Just a possibility, I haven't really explored it in detail.