It sounds like he is just not use to it. I would put him in a halter and short lead. Fill a spray bottle up with water, so you don't waste all your fly spray, and start with the front legs. When you spray the legs he may start to move. Keep spraying but hold him so that he can only walk small circles around you. The point right now is not to get him to stand perfectly still while you spray, just to get use to being sprayed. Keep spraying until he stops moving. The minute he stops, you stop. Then start again. Do this until he accepts his front legs being sprayed and is relaxed. Then pick another part of the body and start all over again.
You don't have to be crazy to work in a barn, they'll train you!