Of course, all disruptive innovation starts at the bottom of the market. I am sure the first big wins will be giving educational access to talented and bright but poor kids in the developing world. For them, even something like access to a first world university is far from affordable, and the fledgling online classes are much better than the alternative, even if they aren't yet competitive with traditional university education.
I took the online ml-class last semester, and I am now taking the pgm-class this semester. I have or am taking graduate versions of the same classes at a traditional university.
The big discovery (thanks to Sal Khan) is that teaching fundamentally scales. It's a big waste that all over the world, there are hundreds of smart researchers each teaching 10s to hundreds of students basically the same subject. What would be best is to get one great teacher for each of the subjects of those 100s researchers, make him focus really hard (10x the effort he would have put in, but 1/10 the total effort of all of the previous combined effort) to make a ridiculously good online class. Then you have freed up a bunch of time for the researchers, and most of the almost thousands to 10s of thousands of students are actually experiencing a better class.
Why is it that people (even apparently faculty like Thrun) seem to forget that universities deliver more than just undergraduate education? "Delivering higher education" also means research labs and centers for scholars, graduate education, professional education, executive education, etc. While undergraduate education may be ripe for disruption, there is a serious leap needed to go from there to the complete disappearance of thousands of institutions.
Just look at the numbers: dederal research grants and endowments will sustain at least several hundred universities for the long-term, and other universities that are currently teaching-focused will move more of their efforts to research as students take online classes and stop being paid customers.
The institutions that should be worried are technical colleges (depending on major), community colleges and perhaps state college systems. They are the most likely to be disrupted, particularly if Udacity could offer a more comprehensive curriculum. But Stanford? Or even schools like the University of Florida or UC-Santa Barbara? They have plenty of other income sources, and still have a lot of life in them.