TW had operations in those cities dating back to the 50s, and large staffs that were necessary for daily 747s. Downsize to 767s (which is all the traffic that exists) and you're too big for your traffic.
Supposedly, though, in Europe you can't downsize easily, so you have to close up shop. Gossip has it that they'll be back to Madrid and Rome from JFK and Frankfurt to STL within a year (assuming all goes well and they get a few new planes). Also, if they closed the cities then Carl Icahn couldn't sell lowestfare.com tix there--but if they come back it's a new city and he's not party to it.
Jl