I did think about that, and I have. I briefly considered getting rid of my car to eliminate the cost of insurance and renting a parking space while working from home. It was at best break even to match my then current behavior with public transit and taxi-equivalents.
It seems about 40% of Caltrain is not covered by fares.
It's hard to find numbers, but it seems like as well something in the neighborhood of half of road costs are covered by gas taxes.
I'm trying to make the point that these costs aren't hidden and don't come from magic places, they seem to be real and Caltrain seems to be very inefficient compared to what one would expect.
One would expect a train capable of carrying hundreds of people would be orders of magnitude less expensive instead of being more or less at parity with one car per person.
http://www.caltrain.com/Fares/farechart.html
https://www.edmunds.com/toyota/corolla/2017/st-401668011/cos...
A small car that drives anywhere near that distance will cost >$5K/yr
And the most magicky auto costs are the ones hidden a few layers deep, in our city design & abundance of parking for example.
Whereas, with public transit, far more of the costs are represented by the fare.