Well, a quick summary...
BART (short for Bay Area Rapid Transit) is the mass transit system for San Francisco and surrounding cities -- think of it as like the Subway in New York, or the Underground in London, or the Mass Transit improvement you build in Civ to restore the one one city health penalty you lost when you made that coal plant.
A group of people decided to protest the BART security shooting a drunk guy who was trying to attack them with a knife. BART, which runs repeater cell stations so that people who ride it can use their cell phones, initially responded by disabling that cell network to prevent protestors from coordinating their efforts to block the trains from running by climbing on the tracks, but later gave in and kept it enabled.
They did not run trains on the stations where protestors blocked the tracks, as that would have killed the protestors, but the protestors and some commentators here are angry they still ran the other trains, I think. I'm not clear on this part, to be honest.