The only problem I have ever had so far taking pictures (knock on wood
) was taking a picture of a MBTA Flyer trackless trolley at Watertown loop on city streets when the driver told me I needed a permit. I have taken a lot pictures of the surface portions of the T including many of the Mattapan Ashmont line, North Station El and from T property too and have had no problem. I have a tiny Pentax digital camera which helps a lot for quick shots and is very discrete.
This new policy is really a problem for people who are traveling into Boston since I imagine you cant send in a request by mail but have to be there in person then wait the 5-10 days.