I have been challenged while taking photos at Zurich HB and I know of one professional video (REOS) where a similar incident occurred. Once I explained that it was for personal use, they let me continue to shoot.
I did have one incident at Arth-Goldau around dusk (2004) when my flash went off. I had assumed based on my setup that there was enough light to shoot in AUTO without the flash going off. The driver was not amused at having been flashed while entering the station area. I did not get the chance to apologize, but I am much more careful since then.
I have never gotten the finger.
If you know who the train was operating for, that would be the place to start.