A significant component of this is that your (usually free) parking on both ends of the trip is subsidized by its requirement in local zoning, which increases general costs and subsidizes driving (parking spaces often cost $10,000+ apiece to build, excluding any land cost). The Highway Trust Fund, which pays for interstates, has also been bailed out by general federal funds in recent years, and local roads are usually built and maintained by general local taxation as opposed to any tax on motorists.

Diesel trains with conductors also have high opex as opposed to electric trains.

Plus transporting 4 people in a car is a best-case scenario for auto transport costs. And you seem to be making your estimate either assuming a very low TCO car or by excluding deprecation, maintenance, and insurance, since the IRS estimates the average car costs 54 cents a mile to operate.

Beyond that, cities along the Caltrain line have severely restricted development around train stations and forced it to their fringes along highways, which makes train transportation less practical and auto transportation easier.