Mapping is a growing part of the iOS SDK, I can understand Apple not wanting to be dependent on Google for that, particularly after Google started demanding significantly increased fees for Google Maps API usage:
That's the Javascript Maps API, first, and it only applies if you don't have an enterprise agreement anyways. You don't think Apple had a contract for mapping data independent of Google's pricing of their web API?
(for developers, AFAIK there has been no cost for using Map Kit in iOS or a MapView in Android)
http://www.nytimes.com/2012/03/20/technology/many-sites-char...
Google walked back some of the worst effects of the changes:
http://googlegeodevelopers.blogspot.ca/2012/06/lower-pricing...
but by then the damage had been done in terms of Apple's (and developers') perception of the Google API.