http://sanfranciscobayferry.com/
In Seattle it makes sense because it's between islands, some of which have no bridge access. In the Bay Area, there are bridges directly on many routes, and aside from a couple of tourist places, everywhere the ferries run is at worst two bridges or two segments of ground travel away. (In Seattle, the transit authority is actually fairly competent too, by comparison)
The idea of more bridges has been brought up but met with strong "not in my backyard" resistance. A short bridge from Bremerton to Bainbridge would make a lot of sense (and allow two ferry routes to be combined) but the wealthy Bainbridge Islanders are against being connected to the less well off Bremerton.
I looked at Whidbey Island before (and visited; it's nice!), but didn't realize you could actually drive there (even if it's super out of the way).
http://www.sfgate.com/bayarea/matier-ross/article/South-San-...
While basically matching your numbers for the new routes, the article also mentions that the effective subsidy for the older routes is about $15 per ride. I guess part of the question is how to distinguish "start up costs" from "operating costs".
I still found it hard to believe. So I took sfgate's numbers, and did the math.
100,000 riders a year? That's only ~270 riders per day. For an assumption of 8AM to 10PM, it isn't a hundred passengers going across the bay in per hour – it's a grand total of 19.
And for that, they built a $26M ferry terminal?
No wonder it costs so much.
BART and then Uber from 16th st or something seems like the only semi-viable non-self-drive option. Pretty expensive, though.
It would be interesting to see if they could build a floating train somehow (trust me, this is the kind of project that gets you promoted at Google :-) basically float a monorail track between up and down the bay such that you got the energy/operating costs benefits of rail setup without the huge land/tax/easement costs of a land locked rail line.
Unless your endpoints are directly at quayside, a ferry boat service is going to involve at least one, and quite possibly two transfer points at either terminal.
Commuter buses, by contrast, are particularly efficient as they allow passengers to be collected close to their homes, often within feet, or at most a few blocks (in a dense urban setting, as is the case with the San Francisco executive shuttles). Where there's a reasonably direct land route between locations (note that this isn't the case for, say, a Bainbridge Island - Seattle commute, buses are often faster than ferries.
Fuel cost is another factor -- on a per-passenger basis, boats use a considerable amount of fuel, I believe bus service is generally more efficient (low vehicle:passenger weight ratio).
On the positive side: boats generally don't suffer from congestion issues (though weather and fog may slow them down), and often afford more space per passenger with a greater ability to work en route, as well as the option to get out in the fresh air (though a brisk 20-50 kt breeze is rather more bracing than you might be prepared for -- the after-decks are generally quite pleasant though).
As for public-sector ferry services, there are numerous ferry services on the San Francisco Bay, many resurrected following the 1989 Loma Prieta Earthquake which took out a major bridge crossing (the San Francisco - Oakland Bay Bridge), including service between San Francisco and Sausalito, Tiburon, Larkspur, Vallejo, Berkeley, Oakland, Alameda. I've heard rumors of a public Redwood City service but don't believe it's been restarted. Oddly, there seems to be no good one-stop shopping site for information on ferry transit, including http://511.org which is otherwise a transit / traffic information hub. Wikipedia seems to have one of the better compendia, though I'm not sure it's complete: https://en.wikipedia.org/wiki/Ferries_of_San_Francisco_Bay#F...
As I understand it, the Ferry from Sausalito to SF is regularly used, because BART doesn't visit the north. Why there is no South Bay to East or SF I'm not sure, maybe because up until recently there wasn't enough interregional traffic where BART/Caltrain was not already there.
See Bay Keepers: http://baykeeper.org/blog/take-action-help-stop-unwise-devel...
The worst case might be an accident at one of the terminals or a specific boat being disabled.