Quite funny - I know someone who uses a similar setup to send GPS Coordinates for a Quadcopter and a Plane via the audio channel of the video link (he flies the Quadcopter/Plane with video goggles) to the ground station.
There, an Arduino controls some stepper motors to point directional antennas at the copter/plane.
They usually use simple FSK just like the "real life" helicopter in the article.
Here's an example of a common simple protocol:
http://www.flytron.com/pdf/audio_modem.pdf