A couple things:
1) PER is ok as a stat, but it has its flaws and you have to reasonably understand what they are if they stat is going to be of any use to you.
2) You can't just look at PER as your player rater, even as a just off-the-cuff rater, because its perspective is too narrow. Conservatively there are 3 box score "advanced stats" regularly reported on the NBA through the season: PER (Hollinger and B-R), Win Shares (B-R), and Wins Produced (Berri) and at least a couple +/- based stats: On-court/off-court +/- (82games.com), in-season APM (BasketballValue.com).
My point? Each of those has their advantages and disadvantages, and each one emphasizes a different part of the game. PER is generally going to have more volume scorers and part-time role players doing well because they score more per minute (you mention Duncan, but he shoots 14.2 times per 36 minutes vs Rondo's 8.7 shots/36. PER is a per-minute stat, and Rondo plays a lot more minutes without shooting/scoring much). On the flip side, Wins Produced is a lot more about rebounding and assists so I'd bet money Rondo is a lot higher than 47th in the league by that stat. On the flip side Win Shares is all about efficient scoring (i.e. points per shot), so I wouldn't expect Rondo to do as well there whereas Pierce and Ray are probably beasts in that stat. And then the +/- stats give you a perspective on how much a particular player's output means to how his team actually produces.
Bottom line: I wouldn't worry about Rondo not ranking highly in PER. The stat itself isn't conducive to recording the things he does well. But I'd look at a cross section of all of the different "advanced" stats that are out there, and I'd bet that Rondo measures out better than 47th in the league. In fact, in a nice cross-statistical comp I'd bet he's somewhere in the top-25 probably.