Thanks everyone for the comments.

Matt:

Yes, I've heard of Mike's problem and of someone else have a polite and satisfactory discussion with the ST police. I've taken several other shots in the Beacon Hill station, and once in the presence of a transit police officer, with nary a second look. In this case, there wasn't a soul in the station, aside from myself and my son. After the first train arrived and a couple of people left the train and the station, we headed to the north bound side and waited for one train to arrive for a tunnel shot, got on that train and were out of there.

Had a transit officer been present, I'd have either not taken the shot (wouldn't want to have my son, see me have even a polite tangle with the police) or asked for permission.