Most of their customers will grumble about it, and guess what? They'll still buy the next iPhone. Apple's marketing really helps them here.
Most??? You use that word, but I don't think it means what you think it means...
The key aid here from Apple's marketing is that Apple knows who their customers are. The "loss" of the Transit info isn't very meaningful for Apple's customers and frankly it is worse than useless in Google Maps for many people now. For example, Google has incomplete and inaccurate info for the SMART bus system that serves (for a loose definition of "serve") the Detroit suburbs. Are they better in other places? I can't possibly know but I wouldn't ever trust that feature given that I know it to be routinely wrong. Do iOS users actually get anything useful from Google's Transit misfeature? I can't know the answer to that but you can be sure Apple has at least a partial answer and has some grasp on how well such a feature can actually be implemented. My guess is that Transit is a feature that would not be capable enough for enough iOS users to be worth doing. If most iOS users even notice losing transit info as a Maps feature I'd be surprised.
As TFA notes, it is very likely if not certain that Google will be offering their Maps app for iOS 6 independently, or maybe rolling the functions into their existing Earth app. How many people will grumble and for how long? I don't know with any certainty, but I'd be surprised if it is "most" by the standard definition.