It turns out that the no-stroller rule was just a Muni policy, not a federal regulation (though that didn't stop me from writing a Biggie-inspired "Federal Agents Mad 'Cause I'm Flagrant" headline).
Now San Francisco supervisors are discussing whether the anti-stroller policies are chasing families out of the city. (It sounds like they're more concerned about Muni buses than the Metro, though.)
From the Chronicle's City Insider column:
It may seem like a small thing, but Muni’s rigid policy about baby strollers has been a longtime gripe among parents of young children. Currently, it’s up to the bus driver’s discretion about whether to allow a stroller on board at all. (Imagine the outcry if that was the policy for wheelchairs.) If it is allowed, the baby must be removed and the stroller must be folded up. The policy also specifically prohibits parents with strollers from using wheelchair lifts and “special ramped platforms” for boarding a Muni bus.
Oh, and if a parent does manage to climb on board clutching a folded up stroller in one hand and a baby in the other, he or she is given no priority for the seats at the front. So basically, the wheels on the bus go ’round and ’round all over town – with no baby strollers on them at all.
[Supervisors David Chiu and Sean Elsbernd] are “urging” Muni to consider permitting unfolded strollers on board as long as they’re not blocking the aisle, the wheels are locked and babies are strapped in. They also want parents with strollers to be allowed to use wheelchair lifts to board buses and to receive secondary priority for the prime seats after seniors and disabled people.Elliot and I rode Muni buses everyday when we lived in San Francisco, but I have mixed feelings about this idea. First of all, bringing a stroller onto a bus is a hassle for pretty much everyone (you, your fellow riders, the bus driver). You're better off carrying your child in a Baby Bjorn or a sling.
As for getting priority on buses, I was apparently perceived as such a barely competent dad that people went to extreme lengths to clear a space for me. I never had an issue getting a seat. In fact, I had to fight people off to let me stand.
So if you run into trouble, dads, just act like a bumbling nincompoop.
Sorry, I have no advice for moms.