I'm on Team BART
As a San Francisco resident, I'm not 100% on BART's side (the phrase "chilling effect" comes to mind), but mostly I support this course of action for two reasons:
1) The protestors are supporting a guy who assaulted a police officer with a knife. Suppose it had not been a cop but some random person who happened to catch the drunk's eye and gotten knifed for his trouble . . . would that person have been wrong to defend himself, even to the point of using lethal force? If you use a lethal weapon to attack someone, you are, in my opinion, implicitly placing your own life on the line--the victim always has the right to self-defense.
2) Most people who use cell phones on public transit are douchebags (no, I know that YOU'RE not, you're a world-renowned heart surgeon who can't possibly be interrupted for a few minutes; I'm talking about those OTHER people), so blocking their cell phone service for 5-10 minutes (about the length of time it takes to get through the affected area) is a mercy to the other passengers. If BART could figure out how to shut down the ability for people to play music on their cell phones' speakers, that would be even better.
For the most part, I call it a win-win.