Agreed.Between SFO and Embarcadero, the only view of the bay is at the airport prior to going into the subway portion up to Colma. Between Colma and Glen Park there are some locations where the Pacific Ocean can be seen in the distance to the left (inbound), assuming the oft-present fog has not rolled in.
I always used to get off at Terminal A and get on at Terminal GThanks chakk, did mention that the Thruway bus is one of our favourite rides but it took the first time to work out it's bus right to get the best view. Was also thinking of the Samtrans bus, may give that a try. The bus stop at SFO is really in the bowels of the airport, you would have to know it's there.
The only definite one I remember while taking BART trains, was that you can see the bay and the industrial docks for a brief bit of time between the eastern end of the BART Transbay Tunnel and the West Oakland station. I think there are a few brief moments where you can see the bay somewhere not far from Daly City, and somewhere on that line before you get to SF Airport station.The BART line runs below ground for some of the time, can't quite remember which portions. I don't recall any great views... ?