So I whipped-up a rough flight controller for FlightGear using Accelerometer-Simulator (AccSim) and Mono. With this bridging application, you can control the roll and pitch of your aircraft using any iOS device that can run AccSim. One caveat right now is that, at least on my machine, it chugs the system down to one frame per second. I have a feeling that this has something to do with the way FlightGear's internal modelling system runs, or it's because I'm continually shoving data down it's throat as fast as the socket will allow … but that's an optimization for another day.
The provided socket interface to FlightGear is pretty neat, and I could definitely see creating a native app on the horizon if I thought there was any interest or money in it. Being able to control your autopilot, flight controls and aircraft systems through an iOS device would be pretty sweet.