In the bigger picture, Apple's top two smartphone competitors build transit directions into their mapping solutions. Apple can't afford to leave transit the exclusive domain of third-party developers indefinitely. To use Joel's phrase you're "picking up nickels in from of a steamroller". You should expect to get Sherlocked eventually.
But you're right about being aware of what apple may do in the future. I'm not convinced they'll add public transit (back) into their core mapping app though, as you imply. I think apple has made the decision to optimize for drivers, which tends to be the majority especially outside of huge cities.
Have you guys taken investment before?
Sam, with your resume you should be able to get a+ angels that could help with the business end of things. You guys have the product end covered :)