The question shouldn't be "How well does Khan Academy teach" (well, maybe someday). The important question right now is "Is Khan Academy a better learning tool than most high school and college teachers?". In my experience, the answer overwhelmingly is "yes".
I did have some truly fantastic teachers/professors on the way to a STEM degree, but they were rare. Most were terrible to mediocre, even at a semi-prestigious university. Khan Academy has greatly reinforced my understanding of some subjects, and it's been exceedingly easy to learn some new subjects.
So yes, it doesn't stack up to the top tier teachers and probably never will. But that doesn't matter, because there aren't all that many fantastic teachers and Khan Academy is better than the rest.