I've thought about writing one. The terms the app store policy states "Apps that use location-based APIs for automatic or autonomous control of vehicles, aircraft, or other devices will be rejected". I imagine this is because the iPhone can quit an app at any moment due to a call, memory, etc and if you're vehicle suddenly loses its brain you could imagine the crash that could occur. However that is really saying the iPhone or iPad can't directly control the plane itself. If it was used to program waypoints on the ground and just monitor the planes progress I'd hope that would be alright.
Would there be enough interest though and would such an app need to be open-sourced or could it be a commercial product?