I've found with my Xbox One Controller it has to be turned on and connected before I launch the game. Also that it doesn't have a function in the main menu, you'll need your mouse to start the game in either Single player or Multi player (but the pause menu works fine with it.)
If you turn it on/connect it while the game is already running, restarting the game should have it recognize it.
Just for information, I use an Xbox One controller with the wireless adapters and Windows 10 as my OS. This may be of influence in your case.