Fortunately bikes (and even e-bikes!) exist.
Edit: Also Google Maps says San Rafael to Palo Alto will take 2 hours give or take a few minutes on public transit, with 3 buses, but the middle one you could easily cut out with a bike or a 4 block walk. That doesn't really seem absurd at all for an occasional trip. People do 2 hour drives for an occasional trip and no one bats an eye.
1 year ago, I lived in San Rafael (Marin county, Bay Area). I occasionally needed to go to Palo Alto for work meetings. The fastest public transit option was to take a 40 minute bus to Larkspur Landing, then a 30 minute ferry to the SF Ferry building, walk for 20 minutes, and then take Caltrain for 45 minutes or more and then walk from there. With transfers, at minimum it was a 2.5h journey, but typically 3+h
All to cover a 60 mile / 100 km distance