I think that in the early shorts the Roadrunner was oblivious. He just wanted to run around, and the Coyote's suffering was the direct result of his own mischief. Acme karma. However, sometimes in the later episodes I did get the feeling that the Roadrunner had some understanding of what was going on. Maybe over the years he caught on, but continued playing dumb because it's so fun to see that dumb coyote clobber himself.
Regarding the question of what a protagonist is, I may have to rethink my nomination of Light Yagami from Death Note. He's a main character, but is he a Good Guy or a Bad Guy? From the very beginning he blithely kills people because, in his personal opinion, the world is a better place without them. He feels he can create a better world by taking out the trash. But then he kills good people because they are trying to bring him to justice, and by the end his power has utterly corrupted him, turning him into a madman in his final scene.
Maybe I'll switch my nomination over to Misa Amane from the same series. Many people will see her otherwise, but to me she's vapid and irritatingly bubble-brained. There are times when I want to throttle, and when Aizawa does a slow burn in one scene and then finally shoves her out the door, I mentally cheered.