I think it's easy for us to underrate Rondo's defense because we see the gambles he makes, and also because PG is the hardest position to assess for man-to-man defense, because PGs are screened off plays much more often than any other position. Fighting through those screens is part of good defense, but realistically a lot of the points and assists an opposing PG gets aren't the fault of the other PG. So it's easy to overestimate how many defensive failures Rondo has had.
Also, as others have pointed out, much like Dwight Howard affects a lot more shots than he actually blocks, Rondo disrupts ball movement and penetration even when he never gets a hand on the ball. Defenses know he's there, and it often makes them tentative or rushed, which produces a lot of turnovers and bad shots, even when Rondo didn't explicitly do anything good on the play.