Not that I'm justifying it, but it's a post-9/11 thing. After the attack, the city really cracked down on filming in soft target areas like bridges, tunnels, and especially the subway. Part of the reason was that videorecordings and photographs of NYC infrastructure were recovered from terrorist staches domestically and abroad. The videos were being studied in order to figure out where to place explosives or biological agents. I can't remember how many times I saw muslims or middle-eastern-looking men being detained for filming subway tunnels on the platforms after 9/11. Happens all the time.
I left NYC about three years ago, but NYPD always took a heavy hand against that kind of filming, even in 2010.