In some cases, you cannot get a navigation system unless you buy the vehicle's higher, more expensive trim levels.
Thieves will have a much harder time stealing a factory navigation system than they will a portable unit that's stuck to the windshield with a suction cup.
Resale Value: Factory navigation systems may improve a car's resale value, but only within a few years.
Furthermore, there are now lots of alternatives, ranging from portable systems to smartphones to aftermarket stereo systems with nav. These systems typically have larger screens that are mounted in well-thought-out locations and are designed to work seamlessly with the vehicle.
This means that you can use such factory features as voice activation and other interface methods like control knobs or on-screen buttons.