I am new to LOMAC but like it so far. When I want to fly a mission in the FBP it seems I cannot take control of the plane I am to fly. I checked the options, but for some reason I cannot fly my plane. My joystick works good in the training and open mission. Any suggestions? Thanks.

Well, the FBP should default to making one aircraft set to SKILL = Player.

So unless you are changing that so that both sides are AI (Average, Good, High, Excellent, Random) I'm not sure why you cannot get into the cockpit of your aircraft.
Have you tried pressing F2 external view until you see the external of your jet then pressing ALT/J to Jump into it?

Also makes sure, (dumb suggestion, I'm starting to think,) make sure you also selected a flyable aircraft. They are the ones highlighted in orange.