Flying isn't heights.... your feet are still on the floor.
Is that the difference? I dunno!
On the other hand, we flew a few times - just rides, really - in tiny aircraft. My grandfather's company had a small plane, so they'd come up from Indiana to visit in a little four or six passenger plane. Those freaked my brother out, too. We talked him into taking a ride once, and after one look out the window, he spent the rest of the flight white as a sheet, holding onto the seat with sweat running down his face.