I know enrollment is way down in my Master's program. Still, I find it hard to believe that online sites and programs are the primary reason for such a decline. I have no doubt many of these programs deliver quality content. At the same time, when one enter's the job market, the rigor and above all brand name of a good Master's program is invaluable in the job market. I wouldn't trade it for a bunch of videos from the Khan Academy.
It depends on the kind of skills that you want to get after graduating. Long term a masters degree definitely pays off. Short term? Well, if I can learn half of the Adobe suite, CAD, and some business skills in a month or two for less than the average textbook costs, why would I bother with getting myself in even more debt?
Physics graduate programs are increasingly offering a fast track to a PhD, straight from a BS. Some people might benefit more from an additional couple years between the two, but typically once you've done your PhD, the doors of your choosing begin opening rather easily.
I think that masters degrees that should never have been masters degrees are on the way out. Anything that can be learned from Khan Academy on your own is NOT what should be in a Master's level program, And I say that as someone who loves Khan academy, SciShow, Crash Course, etc. Master's degrees should not be basic education, they should be deep work on specific subjects, the way that Doctorates are treated now. Doctorates should be a magnification of that.