Atticus accepted Tom Robinson's case because he knew no one else would want to take the case, and if anyone else did, he wouldn't put on a good case or care whether Tom was convicted. Atticus knew the odds of getting Tom off from the very beginning, but he knew that he had to try. Taking these "baby steps" was the only way that racial bigotry was ever going to change in the South. Atticus knows Tom is innocent, and if Tom was white, he would have been found innocent with the evidence Atticus presented. Atticus at least made the jury deliberate for a while before bringing in a guilty verdict.
In my opinion, Atticus accepts this case because that is the kind of man he is. It is a case that goes along with his values and so he thinks it would be good to take it.
Atticus is a man who thinks that it is wrong to bully the weak. He does not like it when his kids torment Boo Radley, for example. And he does not like the way whites treat blacks in Maycomb. So I think he is taking the case to try to prevent Tom from being abused due to his race.
Atticus is a man of integrity. He knows that a black man in the south is not going to get a fair shake. He is asked by the judge to take the case. He accepts because the judge asks him and because he believes it is the right thing to do.
Atticus tries to install in his children the principles that he believes in. One of those is that one must stand up for one believes is fair. His actions speak louder than his words. His way of teaching the children is by setting an example. His taking on the Robinson case is just another example of his good qualities.
Atticus took up the Tom Robinson case because he knew no one else would accept it. Atticus did not only look at outside features, but Atticus understood that Tom was innocent. Tom is black so he would not be able to make his own argument on that case, however Atticus was aware and took up this case in order to give as much help to Tom as possible.
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