Make sure you have enabled the joystick in the "Joystick" tab of the Orbiter Launchpad dialog.
The joystick is usually mapped to the reaction control system (RCS) or aerodynamic control surfaces of your spacecraft, so remember:
If your joystick has a throttle control, you can use it to manipulate the main engines. If your throttle control is not responding, try selecting a different throttle axis from the Launchpad dialog.