Andy Baio clears up some of the confusion regarding maps in iOS 6. It’s comprehensive, well written, and hits the nail on the head regarding mass transit directions:
Why is Apple doing this? Do they hate public transit?! Of course not. Transit directions aren’t in iOS 6 because Apple replaced Google’s maps with their own solution, which didn’t include access to transit data. Maintaining transit feeds and keeping it up-to-date for hundreds of cities was presumably too difficult to attempt for this first release, so they decided to outsource it to third-party apps.
There are hundreds, perhaps thousands of transit agencies in the United States (not to mention the rest of the world). That’s a lot of agreements to ink. Once Apple gets those worked out, I expect mass transit directions will return.