Any kind of applied research in the US academic sector these days is best understood as corporate R & D for established interests in pharmaceuticals, technology, industrial chemistry, etc. You're certainly not free to do blue-skies renewable energy research (budgets for that are still miniscule at best, and have been since the 1980s), for example. The job description has become indistinguishable from that of in-house corporate researcher - narrowly defined assigned problems are what you get to work on, and 'academic freedom to pursue the research wherever it leads' is a quaint myth.
The obvious fix is to eliminate exclusive licensing of academic IP (i.e. repeal the 1980s Bayh-Dole Act), which would force corporations to spend capital on their own private R & D divisions if the wanted exclusivity, and simply make any university-held patented discovery available to any entrepreneur who wanted to develop it for a small flat fee.
Until then the author is 100% correct about entrepreneurship being the only way out of the trap.