95% of the time when I see a rat in the subway it's down on the tracks where there's way it's going to bother any people (except straphangers who are so freaked out by rats that the mere site of one makes them shriek).
Occasionally I've seen them on the platforms, where they're usually scurrying between holes in the wall or garbage receptacles, doing their best to stay as far away from people as possible. I once saw a dying rat lying on the platform that didn't seem able to run away. On another occasion, I had one run towards me until it got within a few feet. As soon as I moved, though, it froze, reconsidered, and ran back to the nearest hiding place.
In this case, it sounds like the rat managed to get on a train, which I've never seen (pigeons, yes; rats, no). My guess is that it was far, far more afraid than she was, being on a crowded train full of people. It was probably looking for a nice dark place to hide when it ran up her pantleg. Then we she started moving, it probably started scratching trying to find a way back out. All speculation of course, but the idea that it "attacked" her seems unlikely.