I have had a couple of dogs with ongoing ear problems and it isn't any fun to treat. Maybe after the vet cleaned his ears they are really irritated and will feel better after some time passes. I just had to leave my dogs ears alone for a couple of days till they were not so inflamed. My aunts dog cried and cried when he had his ear drops put in - finally found out he was allergic to the drops and it was raw inside his ear!
My vet also had me use oral benadryl to help with the allergy ect. You might want to check with your vet again and see if you can give him something to help. I don't like to medicate my dog unless needed but it can be very tramatic to get the ears cleaned (they have even had to put my dog under to get the ears cleaned) if you have ever had a ear ache you know what I mean! And you need to have a way to get the ears done without the dog being in such fear it may bite.