When BART was built, the original plans called for elevated structures through the Berkeley area. The people of Berkeley voted to tax themselves to pay the additional cost of tunneling, and that's why the Berkeley stations today are underground. I would have a great deal more sympathy for those people demanding that the High Speed Rail line be built in what is clearly the most expensive method possible if the people of the area expressed any willingness at all to pay the marginal cost of undergrounding the line. But instead, what we hear is a bunch of hysterical fear-mongering about massive walls destroying cities. Well, there's an elevated grade separation running through most of San Carlos and Belmont, and as far as I can tell, those cities have not been turned into smoking ruins divided like Cold War Berlin the way some people seem to think an elevated HSR line will do. For that matter, BART runs through much of the East Bay on an elevated structure and I never hear of the Great Wall of Hayward or of the Death of Fremont because of it.
The hysteria over High Speed Rail makes a mockery of any claims to being environmentally progressive or "green" by the people of the Peninsula. A high-speed rail line will carry more people more quickly and efficiently than a freeway or an extra runway at SFO, removing cars and airplanes from the roads and skies and giving us all improved mobility options. If the experience of the Japanese and Europeans is anything to go by, as soon as the line is built, the question won't be "why did we build this," but "when will we expand it?"
(Lives in Fremont, works in San Mateo, and wishes he had a viable rail alternative to commute to work do he didn't have to drive and clog up the bridges.)