I started flying young and by myself, but always loved it. I still love flying very much but have anxiety related to the taxi-ing before and after taking off and landing related to an incident I dealt with.
I suggest first to find out why he's afraid. It's much different to be afraid of being so high up in the air vs. being enclosed in a small space with no escape vs. being afraid someone bad will be on the plane vs. not liking the feeling in his head when his ears are "stuffed up". Some you may have to just face (no way to fly without being thousands of feet up in the air), some you can explain (that we have the TSA and they protect us from anyone bad getting on the plane), and some you can mitigate (gum and meds like Benedryl for stuffy ears or noses).
Then, do talk to the pediatrician; a phone call should do. Sometimes they will tell you to try Benedryl before boarding the plane, or once seated. Sometimes they will have the child take it the night before.
If nothing sounds appealing to you, you can then do distractions, distractions, distractions. A comic book or book is great to read while taxi-ing before takeoff. Gum helps ears pop on the way up and down, but I chew throughout because I like gum.

Once you're in the air, there's nothing like a specially picked out movie - especially one he's picked out himself and never seen, or a favorite that always makes him happy. Apps on an ipad/ipod, or a video game console like a DS or even a GBA (I still take mine sometimes) keep the mind stimulated and actively focused on something else. A new book is also great for readers. Travel games work well too.
I would not ask him "how he is" during the flight, because if he's not scared you'll remind him, and if he IS scared, he'll have to talk about it. Let him tell you how he's feeling, because he WILL if he's having problems.