Throughout the trial, Atticus presents irrefutable evidence that Tom Robinson is in fact innocent, and yet when the verdict is handed down by the jury, he is convicted. The jury is made up of the men and women of Maycomb and their decision shows us that no matter what the truth is, they will never give justice to a black man when it contradicts a white man's word.
This is reinforced later on in the story when Tom is killed. The citizens of Maycomb are simply unable to do what they know is right. The seeds of racisim and desrimination in the town are simply too deep. Both Scout and Jem are disturbed by this. Jem cries when the verdict is handed down.
Eventhough Tom is convicted, the important thing is that the town knows that Tom is innocent. It is step towards the end of racism.