Just wanted to throw this on here for anyone who was stuck in the same situation on Linux with the game not detecting joysticks. This is by no means a proper fix but a work around so you can use a joystick.
Basically you can map a joystick that is detected and properly configured in Linux to any mouse or keyboard functionality the game supports. It runs in a task tray and you can setup and select different profiles on the fly.
Takes some fiddling but no more than anything else in Linux and works very well.
If you have a older joystick like mine (CH Flightstick Pro) be sure to use 'jstest' or 'jstest-gtk' to calibrate, that way the proper values are being reported e.g. 0 to 32767 rather than 0 to 255.