“The new Transit APIs, referred to by Scott Forstall at 108:58 in Monday's keynote, allow developers to register their app as a directions provider for routing directions for a particular set of coordinates. It will then be displayed in the list of available third-party apps for transit. Clicking a transit app launches that app, passing the start and end values to the app. Contrary to other analysis, transit routes can't be displayed inline from the Maps app.”
This seems to me like a clever move, this way Apple won't have to collect all the data.
http://waxy.org/2012/06/busting_the_ios_6_transit_map_myths/