Welp, guess I'm on
a lot of lists then.
White privilege? Too funny
In all seriousness, there are ways to do it, and ways not to do it. (I'm also white and appear neutrotypical, and well aware of the privilege those grant here.) For one, you don't take pictures of people, particularly transit personnel, except in tourist areas or where others might likely do so. (Taking a photo of the crowd at Park Street, fine.) For two, unless there's a particularly compelling reason not to, make it extremely obvious that you're taking photos. That says to others "I clearly think it's acceptable to be taking this photo, and I'm not trying to be secretive about it, so you can be sure I don't have bad motives." A friendly wave to the bus/train operator, conductor, etc goes a long way too.
I've taken a lot of photos of potentially sensitive subjects - construction sites, shots down tunnels from the end of platforms, electrical substations, yards, abandoned stuff, bridges, etc. Only a very small number of times has anyone taken exception to it. Once I was on top of a parking garage for a while; the attendant was kind enough to let me stay a few more minutes for the photo when I explained. And when I entered
an abandoned tunnel in Clinton, I did get stopped by the local cops and a statie. They were largely concerned about the nearby reservoir, and making sure my companion and I weren't about to graffiti the tunnel.