Aunt Alexandra feels sorry for Atticus. In fact, she says, "I'm sorry, brother." Scout notices a serious tone because she'd never heard Aunt Alexandra call Atticus "brother" before. She is also worried about Jem, who had been crying on the way home from the courthouse. An interesting point to note is that while Aunt Alexandra wants the children to learn the social stratifications of Maycomb and the Finch family's place in it, Alexandra thinks the drama of the trial is too much for them:
"This is their home, sister,” said Atticus. “We’ve made it this way for them, they might as well learn to cope with it."
Alexandra is intent on getting Scout to act like a lady and not to associate with poor people like Walter Cunningham Jr., but Alexandra suggests to Atticus that the trial might be too much for the children. Although she is generally looking out for the emotional toll it might take on them, she is also showing some hypocrisy here. She wants the children to acknowledge the overt social class distinctions in Maycomb but she thinks the unspoken (sometimes spoken) racism and injustice that follows is too much or inappropriate for them.
Alexandra knows that Atticus was the person for the job but she would rather have had someone else defend Tom because of the toll it took on her brother and his children. Atticus believes that the children should know everything about the social aspects of Maycomb.