Over here there is a mixed bag about shooting in sports stadia. I've seen lots of folks do so in Yankee Stadium at baseball games - although I'm told you shouldn't use a lens over 200mm (has to do with copyright laws - not security issues).
There was a thread here a while back that said the NCAA was peed off with a web-based photo service that was posting "unauthorized" pics at college basketball games - not sure where that's going.
As to the original issue, whether one likes it or not, whether one agrees with it or not, the US is in a war (or several of them). Transit systems in particular are considered vulnerable targets and security personnel are under high alert.
In these circumstances, I think the BART cops acted quite reasonably. They didn't seize honus's camera or equipment. They "satisfied" themselves that he was not a threat and let him go on his way.
What would you have done in their position?