The new Google Maps app on iOS -- unlike the pre-iOS 6 Apple Maps app using Google Maps data, is a Google-branded application that integrates with Google Accounts for cross-platform history and other purposes, provides feeback mechanisms that helps Google gather information to improve the Google Maps experience for all users and all platforms, and integrates with Google's reviews and other Google services.
Android, for Google, is a way to drive the entire mobile marketplace in a direction which supports Google's online services, which by design are not tied to a particular platform. Apple may use services to sell the platform, but for Google its the other way around.
If people go to Android instead of iOS, that's good for Google, sure, but its almost as good for Google much if people use Google services on iOS. Heck, that's why Google was best friends with Apple when the initial iPhone with its everything-is-web approach was released.
Google Maps on iOS exists for the same reason that Youtube on iOS, Google Chrome on iOS, and other Google apps on iOS exist.
