LockandLoad,
Lets make sure your joystick is properly calibrated. We're going to do it in Windows first. If you had to load software when you set-up your joystick it probably created a program group. Go to start/programs and look for the manufacturers name and a set-up or calibrate application. It should walk you through calibration and allow you to test it afterwards to make sure everything is working correctly.
If there is no program group go to start/run/control panel and look for a game controllers icon (it might also be under input devices). Double click it, make sure it "sees" your joystick then run calibrate. It should walk you through calibration and you should also be able to test it afterwards to make sure everything is working correctly.
Now go into the game. Go to set-up, controllers, calibrate controllers. It will walk you through calibration.
Next go to set-up, controllers, map controllers. If I'm not mistaken the x axis = elevators (up/down), y = ailerons (roll left/right) and z = rudder (turn left/right). You can also map your throttle to your joystick slider here. Once you've done this click on one axis, click the advanced tab and make sure the scale input sliders are set to default (left one at the bottom, right one at the top and the rest in a straight diagonal line between them). Do this for each axis.
Now go out onto the runway in a fighter. Take off with auto take-off and at full throttle. Make sure you hear the gear bells and see the gear light go off. Make sure flaps are all the way up. Soon after take-off you should be climbing at ~150 mph.
Once you gain a little altitude, level the nose and you should start to pick up speed.
If you've done everything right at this point you should be flying.
Let me know if it works.