He's gotten better about it.... we can now cup your hand over the whole ear and rub, the way labs like, if you do it careful. He doesn't enjoy it, he gets this worried look on his face and looks right at me, but he'll tolerate it. We can pet over the outside of the ear in stroking his whole head. But if we grab the ear flap at all (when I grabbed it the first time, it was to rub-flop his ears the way my old lab used to like) he cries out and recoils.
All you can do with a pet with a "history" is be extra nice to them to try to make it up . . .