I fought this same issue with Routesy, my SF iPhone app, in 2009. Getting agencies to be smart about making data open is a challenge, but a lot of cities are coming around.

Once agencies realize that they can not make a killing off apps and that they're better off having developers make great apps that increase ridership by making the systems less awful to ride, everybody wins.

If you're curious about the story of my battle and how I had to get a lawyer involved to get Apple to let my app back into the store, check this out: http://sfappeal.com/news/2009/06/who-owns-sfmta-arrival-data...