I think the real point is that while Rondo can improve in areas of his defense, it doesn't make him a worse defending PG relative to his competition. Just because he is the best or one of the best defending PGs doesn't mean he is a perfect defender. Sometimes he is lazy, sometimes he doesn't close out, and sometimes he doesn't fight through the pick, but advanced stats and even my personal "eye test" have him ranked at the top.
I'm honestly shocked at the amount of people who complain that Rondo doesn't stop dribble penetration. We all remember that Rondo is point guard and defends other point guards? Their job is to be able to penetrate any defense. The main job of a point guard on defense is to wreak havoc at the top with help defense and make sure he doesn't funnel an offensive player to his strong side or the weak side of our defense. There is barely such a thing as stopping a point guard's dribble penetration in the NBA without proper help and rotations, which Rondo is smarter than almost anyone at doing.
If the fact that Rondo is a flawed and seemingly inconsistent defender makes it difficult to accept that he's the "best defender" at his position, I think it says more about the role that point guards have defensively at this point in time.
The league so heavily favors quick, athletic ballhandlers, that the best a defender at that position can do is try to gamble and get steals by jumping out in passing lanes and playing as risky as they can without being an outright sieve as far as allowing dribble penetration is concerned.
When I watch Rondo it's not often that I think, wow, he's dominating on defense, the same way I might feel that a great center such as Gasol, Howard, Asik, Noah, or Hibbert dominate on that end. But I can't say that any other point guards come to mind that have a more noticeable impact on defense, unless you want to count Avery Bradley as a point guard.