Atticus remarks that of course he will defend a negro, named Tom robinson, explaining to Scout that if he didnt he wouldnt be able to hold his head up around town or be able to ask Jem and Scout to do what he tells them. Scout ask, "Atticus are we going to win it?" atticus says "No, hunny... because we were licked a hundred years befor we started, but thats no reason for us not to try to win." and Atticus is a practical man remarking that "We're fighting our friends, but remember this, not matter how bitter things get, they're still our friends, and this is still our home."
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Just as you said above, Atticus knows prejudice is a sickness that is too ingrained in these people to be cured overnight. Atticus knows that someone has to attempt to do the right thing, even in the face of overwhelming ignorance and odds. Atticus has the fortitude, education and empathy to do this. His actions become a testament to his children and the town. Perhaps then, there is hope.