You've done a great job of summing up one of the reasons that public transit in the US is as bad as it is.
My goal is to safely get from Point A to Point B, and I don't want to spend a lot of time waiting around at Point A, or sitting and waiting on the way to Point B.
We have three goals here, in order of importance. Let's call them safety, convenience, and speed.
Taking a bus with a bunch of drunken hooligans doesn't help much with that first, and most important, goal. I want my transportation to be safe, and the high crime rates on public transportation in the US speak for themselves.
Interesting experiences are great. Getting mugged isn't, and while I'm not a prime target (muggers don't usually pick on two-hundred-pound guys that spend a lot of time in the gym), five loud, drunk people in a gang is not the sort of situation I want to be around regularly.
Especially if I'm carrying a $1500 laptop and a $600 smartphone.
Convenience, at least here in SF, is also pretty miserable. I have not once had a bus arrive on-time. The trains are usually on-schedule, but conveniently frequent only during peak hours, and they only cover a small portion of the greater Bay Area. Don't even get me started on CalTrain.
If I want to meet somebody and I need to take a bus, I need to add an extra half-hour window around my journey. If you assume a normal tech-person salary, that lost half-hour makes it cheaper to take a taxi for most journeys.
Speed is good for trains; busses, on the other hand, live at the whim of traffic.
Japan gets all of these right in its major cities. I have never once felt threatened on a train, and delays are few and far between.
The tradeoff they make is in manpower -- station employees are everywhere. We tend to not like hiring lots of people in the US, and so public transit stations might have one or two visible employees, and certainly not visible, uniformed personnel at every platform.
This is why cars are as popular as they are. In SF, if I want to go from Pacific Heights to the Inner Sunset, a journey by bus-and-train pushes about an hour. By car, it's about fifteen minutes.
In my car, I have a stereo, air conditioning, and a clean, comfortable seat. Public transit, on the other hand, is pretty filthy here in SF, and for some odd reason they jack the heat up enough so that I need to do a little striptease whenever I get on a train.
All minor inconveniences, sure, but it adds up quickly, and what do I get in return? I'm late, have lost money in the long run, and arrive more often than not in a worse mood than when I started.
I really want working public transit here in the US, but the way things are going, I don't see that happening for at least another decade.