They get a nice cut when someone buys a $50+ navigation app on the iPhone. I don't see Apple making this or any other navigation app a native application and ruining the market that already exists.
They could also get a lot of third-party revenue by wiping out all of the native apps and letting other people sell them. At some point you have to worry about the value of your platform and now they have Android to compete with.
I think Apple's recent acquisition of Placebase, a mapping company, might indicate that they're willing to compete with Google on a navigation app.