I highly doubt he got MBTA approval for the use of their trademark. That said, it's not like he's selling posters of it, in which case his product could conceivably be mistaken for licensed MBTA merchandise.
Judging from the exchanges in his blog's comments, he's a guy who knows his copyright, and has been careful about using the MTA's logo only in situations where Fair Use allows it to appear, and not using in situations where it doesn't.
I can see why he's so pissed, by the way. Having taken the time to understand the rules and operate within them, he's going to take an especially dim view of others who should have, and didn't.