You have to realize that 'getting involved' in cases like the Muni will usually either get the 'good samaritan' shot (along with some others) or will result in the 'good samaritan' going to jail perhaps instead of the potential shooter. That's a fact of modern life. If you're not an on-duty cop, attempting to do something about it gets YOU in trouble not the crazy one. And if you ARE a cop doing something proactive just generates a load of paperwork and a complaint file (by the crazy and his/her friends/helpers) with the person being back on the street faster than the reports can be done.

Personal experience: So most people ignore craziness and even blatant crime as long as they can (or leave as soon as they can), and if they get involved at all it will be (at a safe distance out of hearing/sight of the crazy) to call the driver or the cops to report a situation. In rare cases, there might be a police response; most of the time you have to live with it until the crazy decides to leave or you do. Yes, people have a right to be as obnoxious as they want to be, and you as another rider have to just accept it. Free speech, among other things. Only when it reaches the point of overt violence can anybody else (even the cops, if by some miracle they're present) actually do something about it and get away with it, perhaps. 'Brandishing' just isn't a crime that anybody will pursue in any major urban area or on any major transit line, not just in SF, Homeland Security statements and urgings notwithstanding.

I feel for the guy who was shot, but claiming or implying that the other riders should have done something about the nutcase before that is unreasonable in modern society. Perhaps one could have called the cops sooner (carefully and stealthily), but that's about it.