Hello Ian, I've met you in PyCon before. But I don't know you have a passion in transit system too. I completely agree with you on most points in your original post. Let me contribute a little in this discussion.
I think I am qualified as a public transit advocate and anti-car person. My main commute is heavy rail + bike. It takes about 45 minutes door to door one way, or a little more than double compares to car. This is a huge improvement compare to my previous job that required an over 2 hour one way commute by rail. I also own a car and use it a lot to transport my family of three. Given I have only one car between two adults I can still claim my car ownership is 50% below norm.
While San Francisco is credited as having one of the best transit networks in US west coast, if you ask me to rate it, I say it SUCKS. Besides all the reasons you have articulated, an additional problem in San Francisco is politics. The buses travel at snail speed because they often have stops at every street corner. So every time a rational person sees this problem and proposes 'Hey, we can speed things up if we just change the stop to every two street corner!' Always some activists would come up in arms in opposition, citing it will do much harm to the elderly/disabled/poor people. OK, so no change. The entire city shall go at the same pace as the elderly/disabled/poor people.
I too see PRT as public transit's future. As a technology person, when I first learned about PRT, I immediately recognized it as a paradigm shifting idea, an automatic transport system that perform as well as or better than private cars. Being a public transit advocate, one must first eschew the ideology that car is bad, transit is good. Only then can we understanding the performance difference between a point-to-point transport system v.s. fixed-route transit and find a better way forward.
Another reason I am passionate about PRT is from a humanist perspective. It is very sad to see many traffic accident happens from the convolution of cars, bike and people. People make bad judgments, often putting speed ahead of safety. It is much better to take this risky task away from human hand and replace with an automatic system. Years later when all transports become robotic, we will look back and think how barbaric driving used to be.