I'm having trouble setting up my X52 joystick. When I turn flight assist off my throttle no longer works , I have to use the keyboard buttons to go forward and back. Thank you for your help.

That is the expected behaviour.
Flight-Assist is the only mode that the throttle works in.
When flight-assist is off, the throttle value doesn't make logical sense.

There are two different ways you can set up the throttle in the Joystick settings page. Throttle only works when FA is on, Accelerate works when FA is off (though it's a bit tricky to use). Someone once made a set of aliases that would switch the throttle setting when you toggle FA, but I don't remember where to find it.

X52 isn't the best choice for this game anyway (trust me - I have one that I bought explicitly FOR it... bad move)

Problem isn't so much the throttle modes (which is the case for any joystick/throttle) but that you don't have hats on the throttle that can be used reliably for lateral thrusting... when the strafe cuts out on you in combat, you're in the shit, and it happens a lot.

I just use the joystick portion and the keyboard for thrusting - throttle's no good.

Do yourself a favor and get a pair of two joys - they'll do you a lot more good than a joy/throttle in this game.