What if you are using a Mac?
Viewing post in Controller Issue?
Most probably they are using the same libraries they used for Linux, so it depends on what controller you have. I didn't manage to make mine work in Linux, but it worked out on Windows by launching it from Steam, so my suggestion is to try to add it as a non-Steam game on Steam on your Mac. If it doesn't work still try to tinker a bit with the controller settings in Steam's overlay, it might help!