The Central Subway has three underground stops: 4th & Folsom (Yerba Buena / Moscone) is the closest underground one to Caltrain. The tunnel emerges under the I-80 and has an above-ground station at Caltrain.
Caltrain's DTX (Downtown Rail Extension) doesn't connect to the Central Subway either.
I think there's supposed to be a pedestrian tunnel from the Caltrain Transit Center station to Market St. And that would be perfectly fine.
One of the reasons subways cost so much money is because stations are so expensive. And stations are so expensive because everybody nit-picks. In the the United States today large public works projects only happen after near unanimous consensus. The result is that when these projects do happen, they're incredibly expensive in order to satisfy each and every desire.
Just like the OP said--we'll never see another subway line in San Francisco for the foreseeable future because there's too much "community involvement". Everybody wants to criticize and nobody wants to compromise. It's a large problem in the US on the whole, and it's led to paralysis.
