Unfortunately the controller support is a bit spotty, especially on non-Windows platforms, and there is very little I can do to help. People who came up with ways of emulating the 360 pad under Linux were able to get their controllers to work, but not being a Linux guy, I wouldn't be able to say how.
I have long been working on an update to the game that may solve this issue, as well as a whole bunch of other ones (60 fps, larger play window, optional 4:3 mode, turbo-speed, better controller support, redefine keys menu, better game balance etc). Hopefully I'll be able to release it sometime soon.
Linux controller woes should be fixed as of RC6 Update!