A couple of things torpedoed the northernmost and southernmost areas of the initial plan. First, Santa Clara County was mad that the initial stage would only go as far as Palo Alto, and voted to back out of BART and fund the Expressway system. Then San Mateo county figured that they would be funding a system that would be mainly used by Santa Clara County residents and would duplicate the Southern Pacific Rail (now CalTrain) service, so they backed out.

As for the Marin County, once the two southern counties backed out, they couldn’t afford to make up their increased share (Marin had a tiny tax base at the time) and the idea of adding BART rails to the Golden Gate Bridge didn’t seem feasible.

http://laughingsquid.com/1961-general-electric-ad-showing-future-bart-system-crossing-the-golden-gate-bridge/

What Steve said. There was fear at the time that the pullouts started by Santa Clara were going to torpedo the whole system.

In fact, there’s been bad blood between Santa Clara and BART ever since. When they were talking about extending BART to the south bay in the late 90s/early 2000s, there was a lot of political resistance based on this bad blood.

It’s a bummer, given that BART actually operates on a real full-day timetable. Caltrain has certainly improved, but it’s still not something where you can just walk into a station and expect to catch a train without waiting for almost an hour.