Do as much prep as you can and explain as much as possible. Sometimes it's the fear of the unknown that can be scary. When my daughter was about that age, she was excited to go on the plane, but didn't want it to go up in the air. So, I told her we would stay on the ground and drive there - LOL We closed the window shades so she couldn't see out. It worked. Very funny though.
And, if you think she will have a serious problem, ask your ped for an anti-anxiety med. It won't hurt for her to take it. I know many people are going to criticize me for recommending drugs, but a pill going and a pill returning are a lot less damaging than traumatizing a terrified 3 year old.
Also, my kids all had sinus issues, so my doc had me give them Benadryl before flying. It helped with sinus pressure and made them sleepy.
Good luck.