I won't comment on the legalities of copyright (IANAL) or the tactics MTA is using (they may have shot themselves in the foot), but there are very good reasons for MTA to want to keep control of their schedule information and limit third-party distribution.
Yes, third parties can often get information out to the public in a faster and more accessible manner than transportation companies, but there's a right way and a wrong way to do it. I should know--I was responsible for the project that first put Amtrak schedules online, back in the Gopher era and then in the early years of the WWW. We also did online schedules for several commuter rail systems, including MTA's, in those early years.
Most important _is_ ensuring that the data is maintained and kept up to date. Having outdated schedules up for download is worse than having no schedules at all. This is not a matter of 'boo hoo, you missed the train by one minute because you were relying on your iPhone--be early next time' as one commenter put it: sometimes the changes can be pretty substantial, especially as a result of construction projects. And yes, the company gets blamed even when the fault is someone else's.
Second, it is _not_ helpful to undercut the system's own communications department. They may not be as fast as you in putting out an app, but they may have something much more useful in process, such as an app that can link to a dispatching database and provide real-time departure information (see NJ Transit's new Departure Vision beta, for example). With all due respect to your programming skill and interface design ideas, users are usually better off with information direct from the source.
Finally, put yourself in the shoes of the system. When we were distributing a downloadable version of Amtrak's timetable, we had a pretty difficult time trying to convince well-meaning individuals not to repost them on their own boards, and getting the ones who had done so to take down outdated editions. They may be dealing with other people who want to do the same thing as you, and all of this at the same time as they're trying to add new features to the official sites.
If you want to do something like this, either as a public service or for profit, the right thing to do is to communicate with the system and get their permission first. Ranting on Slashdot about copyright, government bureaucracies or about the lousy on-time performance of the system's operating side (actually, Metro-North's on-time performance is exemplary--best in the nation) is not constructive. Find out what is in the pipeline, and if you still think there's a need for the kind of information you can provide or the mechanism for delivering it, make the case to the system's customer service people, and you'll probably get a green light and a good deal of cooperation.
Delaware Valley Association of Rail Passengers