Air rights would still require consent. Subterranean easements would be easier to obtain, but for one above-ground hold out, it would require subterranean construction for great distances in either direction (more if a creek or river is nearby). And earth movement is ridiculously expensive. For one 1.8 mile alignment of the SF-SJ route, a 20' aerial viaduct would cost $265M. A tunnel would cost $894M.
What sane businessman would want to get involved in this? The businessman should find an easier field to make money in.
Why does the port get to have a contract with the road operator? Does everyone get a contract?
My point is that transportation, like defense, is so important to the continued success of this nation, that it mustn't be allowed to fall into hostile/disinterested hands, lest we see how damaging the transportation equivalent of an Enron/WorldCom scam is. If that means a little inefficiency here and there I'm okay with it. I view it as the cost of stability.