Tell him, literally, that you are sorry... you know it hurts, but you have to do it to make him all better. Will he understand what you are saying? no. But he will understand the compassion in your voice. And the love in your touch. And the concern on your face. At the end of the ordeal, give him the chicken (or maybe some salmon, or beef liver, or steak) treats that he wouldn't normally get and tell him what a good boy hs is for dealing with it.
If he is snapping and you feel like you are really in danger (of being bitten), muzzle him during the treatment.
When you apply the alcohol, softly blow on it. It stings when I put alcohol on a cut/scrap, it would sting for him as well... and he wouldn't have a reference point for why it stings. Blowing on it will help soothe that. Do the same for the antibiotics. They probably don't sting, but your dog will begin associating the gentle blowing as a signal that applying the medication is over and he can relax again.
The topical antibiotics may still be needed, but your Vet should be able to prescribe oral (pill form) antibiotics that you can crush and mix with his food.
Can't blame him for being upset afterwards, but holding him for a bit, talking to him and watching TV could help him calm down (and maybe forgive you). At least until tomorrow when you have to do it again....