I've been following the Khan academy since 2011 when I saw his TED talk. I recently heard him on the Diane Rehm show and if there has been any decrease in enthusiasm about the concept, it certainly isn't from Khan. The guy still has a tremendous enthusiasm for the idea.
I think a lot of people see it as something that will vastly revolutionize education and I think that this is the problem. You have to walk before you can run. There is no way that the education system is going to "flip the classroom" over night. Integrating the Khan approach in to your curriculum is something that should happen at a measured pace. There may be unintended consequences if they were to flip all of their math/science courses over night.
So, what I think should happen is that some progressive private schools start utilizing it and then we measure the success and the failures without bias. I think what we'll find is a far more efficient way of learning, but we can't know this until it is properly measured. I'm all for Khan though, it's an organization with a great mission.