You'd be appalled at how much overhead universities take out of research grants (from NSF, DARPA, NIH, etc.) to maintain these administrations (along with legitimate uses, like paying utility bills). 40-50% is not uncommon.
I've long been expecting someone like the NYT to do an exposé on the "dark money" of F&A. It would seem to be ripe given he current discussion of the cost of education.
So when they hear an indirect rate of 65%, they think the university is taking 2/3 the money. When in fact, it's about 1/3 due to how it's calculated.