How would the system determine it is in-flight and thus 
  prevent a maintenance shut down?

You would connect it in parallel with something that cannot be shut down in flight.

If you had a transponder in parallel with each engine, on the ground you could shut down all engines; or for an in-flight fire you could shut down a single engine; but you could not shut down all engines (transponders) while in flight.

  Why don't we track buses? Why don't we track cars?

You've heard of LoJack, right? We track cars worth far less than a jet airliner.