My DS was afraid, too. We even called the airline to find out what would happen if he refused to get on the plane (answer: if he's freaking out, we would not be allowed to stay on). For us, the issue was tied to the 9/11 attacks.
We repeatedly told him how safe it is to fly, how lots of people do it everyday, how the pilots have studied a long time to fly the plane, and how much fun he'd have when we got to the destination. Our pediatrician also recommended some books we could read to him (really they were all about overcoming fears in general). He also advised us that if we showed any fear or apprehension ourselves, it would make it worse.
Our fearful one has flown twice now since then, and though he doesn't like it, he'll do it.