What do you mean? It can't possibly be confusing that there's MUNI, SAMTRANS, Golden Gate Transit/Ferry, AC Transit, Caltrain, BART, Santa Clara County VTA, SF Bay Ferry, etc. And those are just the agencies that take Clipper. Some agencies primarily serve two counties. Heck - a few even cross county lines outside of the primary service area - like AC Transit transbay service, VTA lines going to Fremont BART, SAMTRANS lines going to San Francisco, etc.
Then there's WestCAT, (Contra Costa) County Connection, Altamont Commuter Express, (soon to be) Sonoma Marin Rail Transit, Fairfield and Suisuin Transit, Benecia Breeze, etc. Then there are the free shuttles like Emery-Go-Round, Walnut Creek Route 4, or VTA Route 10 (to the airport). Emery-Go-Round and VTA 10 actually stop by stations served by Amtrak. Then throw in various campus shuttles.
Add to that MUNI operates buses, cable cars, light rail, and historic streetcars. And the Golden Gate Bridge Board operates buses and ferries in addition to the bridge (bridge tolls subsidize their transit services).
Seriously though - you're right that this is one messed up system we've got here, because everyone wants to assert a little bit of control.