Although atticus told scout that he was "simply defending a negro" what evidence was there that this was really not a simple case?

The evidence is that many of the townsfolk don't want him to actually properly defend Tom Robinson and in all fairness he did not believe he would actually win the case but it was important to try. He defended Tom to the best of his ability as he believes it is the right thing to do and that everyone has a right to a fair trial.