Atticus cries after losing Tom Robinson's case, and this is a powerful moment because Atticus is not one to show a lot of emotion, either positive or negative, throughout the book. He is a fairly subdued man.
He knows Tom Robinson is innocent, and he put on the best defense for him that he could. Although Atticus is realistic about the racism that exists in Maycomb and he does not have any reason to really expect that Tom Robinson would be found innocent, it does not make the conviction any easier to accept. Atticus is truly sad about the decision his fellow townspeople have made based on prejudice, and he is devastated that an innocent man has to be punished for a crime he did not commit in light of all of the evidence that exists proving his innocence.
So, Atticus is not simply crying because Tom Robinson has been found guilty; he is also crying because of the reasons he was found guilty.