The problem is that KA (and as you point out, many others) believe that lessons are "delivered". This assumes what Paoulo Freire described as the "banking model" of education and it is fundamentally wrong. People do not learn through delivery and people or organizations perpetuating a banking model are misguided and should be challenged.
The author wants to take learn-math-by-rote to task, and that's fine, but that argument is no more specific to Khan Academy than any other math instruction.
Singling out Khan Academy is link-baiting. It's like if I were to bash the Nissan Leaf for not having the latest in, I don't know, tire technology or something. It would be a true statement, but the Leaf is notable for being an all-electric vehicle, and what I'm talking about is something completely orthogonal to what makes the Leaf noteworthy.