My first horse despised the clippers anywhere near his ears (any other location he didn't care a whit... go figure
). I used wild spot's solution of trimming the protruding hair with scissors. Apparently the judges couldn't tell the difference between my scissor-trim and a clip job... that horse and I won a slew of grooming and showmanship ribbons that way...
I never tried cotton balls, but here's a link: Equine Comfort Pom Pom Ear Plugs - Dover Saddlery.
Not only do they dull the noise, but might help keep hairs from falling back into the ear and causing issues.
Scout seems to love the clippers no matter where I stick them, ears and all. After almost a year it's still a novelty to me to not be fighting and compromising over "show ears". (Note: I fold the ear shut and clip away what sticks out... I don't shave out the inside of the ears)