Distortion of truth
These "protestors" are little more than a flash mob. If they want to protest, why not do so at BART HQ or at the BART police barracks? Why are they inconveniencing (or worse) people trying to get home, pick their kids up from school, get to work, go to the doctor, etc.? In case you're not aware, public transit is the transit system used by the working classes and other regular folks. If your goal is to change policy, protesting by shutting is going to turn public opinion AGAINST you.
Furthermore, it's actually a public safety issue. Much has been made of the hypothetical concerns about someone having medical emergency while cell phone services are shut down, despite there being clearly-marked emergency phones on the trains and platforms. Suppose someone has an emergency while the train is stopped in the tunnel because the protestors have managed to keep another train from leaving the platform? Where is your moral righteousness when you've killed someone who really IS innocent?
I won't deny that police brutality should be taken seriously or that people have the right to protest. On the flip side, the police have historically been very tolerant of protests in San Francisco. I marched in the anti-war protests before Gulf War II: Electric Boogaloo, and the only time the police interfered with us was when we tried to march onto the Bay Bridge, which would have created similar safety issues. I actually talked to a riot officer during one of the more recent protests, and he was remarkably calm about the whole issue. In my experience, the SFPD, at least, are not a bunch of truncheon-wielding thugs. BART police may be a separate matter, since they have less experience and training. As I mentioned originally, though, let us not forget that the person who got shot did so because he attacked another human being with a knife. Setting aside the knee-jerk issue of it being a cop, I think every human being has the right to self-defense and the use of lethal force where warranted. If someone is trying to end my life, I would feel completely justified in ending theirs.
Finally, I live in a neighborhood with a large number of homeless people and a large number of police officers. I've had to call the police on three separate occasions in response to assault, mugging, and a drunken hit-and-run driver who ran down a small child, so I very much appreciate the contribution the police make to my neighborhood. While I oppose excessive use of force, I do respect that they have to deal with the least-pleasant members of society, and I don't think they should have to lay down their lives so that some yahoo can go flailing around with a deadly weapon.