I question the speed necessary to maintain a "competitive schedule". Even though a train may not have as high a top speed as the cars, it isn't stopping for every stoplight, stop sign, slow driver nor traffic congestion. So, a train can make very good time compared to a car in those conditions.
And while it is making good time, the rider is reading a paper or talking on the telephone or napping. At the destination, the rider doesn't have to find a parking space, nor pay for a parking space, nor be concerned for somebody breaking into the car, nor buy gas for the car on the way home.
Even a slower train has big advantages and attractiveness.

What is the signal system required for passengers? Is it more severe than for freight trains? Are passenger stations necessary? Buses don't need stations for most of their stops, although it is helpful if the main ones have parking lots nearby.
Are the standards for tunnels and bridges much greater for passengers than freight?
I thought there was passenger service to Eureka at one time. Was that different that what you're calling "commuter service" south of San Rafael?
If SMART disappears, I think the politicians will take steps to maintain the right-of-way in public hands, much as they did by establishing the NCRA a while back. There may be measures already in place to ensure that.