This is something that will take a VERY long time for him to get over and he may never be truely comfortable with his ears being handled. I would start rubbing him on the neck on an area that he is comfortable with, or even likes (a "green" area). Very slowly start to work your way closer to his head, rubbing and scratching lightly as you go. The instant he begins to act uncomfortable, go back to the "green" area until he relaxes. Keep doing this and eventually, you will begin to move closer to his ears in small incriments. Just make sure that you never go past where he is comfortable and eventually, you should be able to handle his ears without too much fuss. As for doing the clippers, after you can comfortably handle his ears with your hands, start the process all over again with the clippers. There is no easy fix for this problem and it will take weeks or maybe months for him to be comfortable but just don't give up.
Haha, DB, we posted at the same time.
My mare (who I got in Septmeber 09) is really touchy around the ears as well...so that's all I've been doing is being consistent, and working with her comfort level...she's gotten to where I can easily clip her bridle path, and rub all over her head and ears. It just takes alot of time...