I've been wanting to put a Raspberry Pi on a quadcopter ever since I realized that the AR.Drone was too limited and poorly implemented.
It's a bad idea to run everything off a Raspberry Pi running Linux. There are a lot of fine tuning PID-related adjustments every fraction of a second, and Linux could potentially delay the running process and cause you to crash (in the physical sense as well as the computational sense). So you need a flight controller like the Naze32, MultiWii, or AeroQuad that takes care that stuff in a dedicated processor.
How to communicate with a flight controller? The typical quadcopter sends PPM or Combined PPM to the FC. PPM sends pulses of a specific length, with one wire for each channel. Combined PPM is the same idea, but sends everything together and only needs one wire total. This is the oldest, most analog way of sending RC signals, coming from the days of brushed motors, NiCad batteries, and 27MHz radios with ten foot long antennas.
PPM/CPPM won't work with a Raspberry Pi with Linux, either, for similar reasons as above. A delay in the timing of the signal throws the whole system off. It has been done on Arudino and Teensy.
The modern way is to use a digital serial protocol. One of these protocols is called Spektrum, and it's implemented on the Naze32 FC, among others.
The Spektrum protocol has been implemented in Perl with `Device::Spektrum`. Should be hitting the CPAN mirrors shortly.