Fly by wire is controlled by a computer, but the autopilot is controlled by another one and the FMC is another different one. All of the can only be loaded with new software locally via cable, and they are very limited computers, most of them are microcontrollers running custom software and when an OS is required they use a custom one that´s real time. (
http://archive.adaic.com/projects/atwork/boeing.html).
It´s possible to create a custom software and charge it to the airplane? very difficult but possible.
It´s possible to take over the control and fly it where you want to, without the pilots having a chance? no.
Maybe in the next generation airplanes once more complex computers are used.
The most probable outcome is that the computer you have hacked will stop communicating with other systems or it´s own sensors and will crash (the computer not the airplane).