Can I charge for editing footage from a video that was taken during a flight as a private pilot in US?
I'm assuming you didn't do the editing while you were sitting in the cockpit, flying the plane. Charge him whatever you want for your time sitting at home on the computer. It doesn't matter where the footage was filmed, if you're charging him to cut it up, edit it together, and render. Even an aerial photography company will itemize the charges and list digital editing services separately from the filming flight.
Just to be safe, though: Make sure he pays you separately for the pro rata cost-share of the flight. You don't want to take a lump sum and have to explain what part was for the flight and what part was for something else entirely.