Rondo's FTA and FGA are both down from last year, and I'd say part of that is because the team has been completely transformed. We've taken all the defensive players (Perk, TA, Daniels) and replaced them with offensive players (Shaq, Krstic, and Green). Rondo's job first and foremost is to facilitate offense and find his guys good shots--and if you give him more weapons to pass to, then naturally he's going to shoot less and the less you shoot the less you get fouled and the less you take free throws.
The other thing that happened is that Rondo got hurt in early December. If you look at the FTA splits per month you'll see that Rondo's FTA shrank to .5 and 1.5 for December and January respectively. Once his health returned (in February), his FTA shot back up to 2.6 per game, which is right on line with his previous rate from November (when he was last healthy). Rondo's been playing big minutes in March, and has probably re-aggravated his plantar facsiitis problem as a result and his FTA is back down to 1.6 per game this month.
So, if you put things in context, the makeup of the team has caused Rondo's FGA per game to dwindle by 2 shots per game since last season. And if you shoot less that means you're going to get to the line less. Combine that factor with Rondo's injury situation--one which has made his less aggressive taking it to the rim--and it's pretty clear to see why his FTAs are down. This isn't about Rondo's makeup--it's about the makeup of his team and Rondo's health.