San Jose to SF is, by East Coast standards, a pretty long ways. Newark to New York is about 10 miles. SF to San Jose is about 50 - more comparable to New York to New Brunswick or Trenton or Stamford.
Find me a 50-ish-mile distance in the US that is easier to cover by public transit than SF/San Jose. Boston/Providence? DC/Baltimore? Philadelphia/Wilmington? New York/Trenton? Comparable at best, but in all cases, you're generally talking the absolute far edge of regional rail that runs hourly at best.
Ronkonkoma out in Suffolk County is around 50 miles from Penn Station in Manhattan.
Peak LIRR trains take less than 90 minutes, with at least one express train in each direction less than 70. There are 13 peak (arrive 6-10AM) week day westbound trains and 14 eastbound (arrive 5-9PM). The longest gap between trains during the week is westbound between 1:46AM and 4:06AM, eastbound it's 1:21AM to 3:14AM. Otherwise rarely is the gap more than an hour.
The far-end (~50 miles) of the mainline regional rail line in Philly (used to be the R5, I forget what it's called after they renamed it) has half-hour coverage in the mornings for commutes, settling back on hourly during the day. To be fair that is unusually good coverage, but it is certainly possible to do elsewhere.
Part of the difference may be that several of the communities along the R5 near Philly are affluent for the area (or in general, in some cases (Gladwyne)). Transit to poorer areas like Upper Darby isn't quite as nice.
To Paoli (25 miles) they have twice-hourly coverage during commute times. Stretch it out to Exton (30-something miles) and you're down to hourly coverage peak.
Doesn't mean SF has to ape the East coast. There are enough people making the 50 mile commute everyday that a public transport system is worthwhile and can be profitable.
I am pretty sure that if Caltrain went about 10 miles/hr faster, 101 will have fewer cars.
I used to take Caltrain and now drive. The problem is not so much the train being slow, but on reaching your station it's still several miles and a bus ride to your office because the density is so low.
All of those examples except D.C.-Baltimore are from a major city to a suburb or minor city. San Jose is actually a larger city than San Francisco and along the route you'll find half a dozen cities on the scale of Wilmington or Trenton.
San Jose is a bit of a paradox; it's a larger, sprawling city, but it's basically a giant suburb to some extent. It has never been a place for startups, and even most of its resident tech giants are in office parks in suburban areas away from downtown.
Find me a 50-ish-mile distance in the US that is easier to cover by public transit than SF/San Jose. Boston/Providence? DC/Baltimore? Philadelphia/Wilmington? New York/Trenton? Comparable at best, but in all cases, you're generally talking the absolute far edge of regional rail that runs hourly at best.