In To Kill a Mockingbird, by Harper Lee, Atticus is struck deeply about Tom Robinson's case for several reasons.
When Atticus first started practicing law, he had tried to defend two backwoods brothers who were not too bright. When asked if they were responsible for the death the individual they were accused of killing, they affirmed that they had because he had it coming to him. The men, without much of a trial, where hanged for the murder. From that point on, Atticus never wanted to be a defense attorney again.
However, when Tom Robinson's case comes up, Atticus decides to take it. Whether it is easy for him or not, he feels it is his responsibility to provide a good defense for a man most white people around him believe he should just ignore. And even though Atticus feels he won't win the case because the sentiments of the Civil War still run deep and painfully through many of his neighbors and community members, he agrees to take the case. He explains to Scout that taking the case is who Atticus is: how could he have expectations of his children to do the right thing if he himself could not do so?
Lastly, even though Atticus believed he probably would not win the case, it seems part of him hoped that Maycomb had moved forward in time enough that justice might vanquish prejudice. The fact that the jury was out so long allowed Atticus to hope. Atticus was also a sympathetic person who was always telling his children to put themselves in another person's skin to understand how that person felt. I expect that because Atticus could not act in a way that would show him to be a hypocrite to his children, he probably did the same with Tom: he probably tried to understand what it was like for Tom Robinson.
In light of trying to understand Tom as a human being, the last part of Tom's story was the most difficult. When Tom is killed trying to escape, Tom's line of reasoning eludes Atticus. He believed that Tom had a fair chance at winning an appeal. However, it seemed that the idea of being in jail was more than Tom could handle, so he tried to climb the fence to get out of the prison yard. Of course, the situation is more tragic in that Tom had no use of his arm, and climbing was futile if he wanted to escape. Still, the guards shot Tom seventeen times, which was probably the most tragic part of the situation for Atticus. Had there been any doubt before, Atticus had to know in no uncertain terms that nothing in Maycomb had changed.