There are some subtle hints that Atticus Finch may have actually been a white supremacist. He notably admires Henry W. Grady, an advocate of the "New South" based on rejecting the traditions and economy of the antebellum South while maintaining the social inferiority of blacks. He also compares himself to "Cotton" Tom Heflin, a leading proponent of white supremacy in the South who believed that "God Almighty intended the negro to be the servant of the white man." There are also those (such as legal ethics expert Monroe Freedman) who take issue with his indifference towards Maycomb's pervasive racism, callousness towards the conditions of Blacks in the county, and his Knight in Sour Armor approach to defending Tom Robinson.
It is not uncommon to hear Dill's preference for hanging out with Jem interpreted as a childhood crush, and his Childhood Marriage Promise with Scout as his cover.
Theories abound about what exactly is wrong with Boo Radley. Is he mentally handicapped? Has he been traumatized by his treatment by the hands of his father and brother? Is he simply an eccentric with an asocial personality?
Aunt Alexandra is a prime target for this. There are many who take her attitude towards her brother and his children as a sign that she really doesn't like them one bit. The novel seems to suggest that she does truly care for them in her own way, but how convincingly it does so depends on the reader.
Iron Woobie: With the stuff he has to put up with, one could forgive Atticus for just giving up and leaving town. But he never lets all the bad things that happen break him. Even Tom Robinson's conviction, which almost totally shatters his belief in the justice system, doesn't break the man.
Jerkass Woobie: Mayella. While she's a very unpleasant young woman who has falsely accused an innocent man of assault, it's difficult not to pity her. She lost her mother at a young age, lives in poverty and squalor, struggles to raise her siblings with no help, has no friends, endures physical abuse from her father, and it's strongly implied that she endures sexual abuse from her father as well. She came on to Tom because she was lonely and he was the only person who had shown her kindness, and then was forced to falsely accuse Tom out of fear of her father. Also, being treated with respect was so alien to her that she was convinced that Atticus was mocking her when he spoke courteously to her in court.
It's hard to tell when Bob crossed this, from beating and raping his own daughter and falsely accusing an innocent man of it, to trying to kill two kids. Bottom line, he crossed it at some point.
The men on the jury who condemn Tom to death also crossed it with that action, all of them except Mr. Cunningham, the only dissenting voice who was eventually pressured into line with the rest. None of them could have really believed Tom was guilty, no matter what they told themselves, yet they condemned a man who they knew was innocent to die just because he was black and because they refused to endorse the idea that a black man's word could ever be worth as much as a white man's. It was nothing less than state-sponsored, judicial murder, and they all get away with it, too.
Boo Radley, as played by Robert Duvall, in his first film appearance ever. He is onscreen for just a moment, and doesn't utter a single word the entire time, but manages to say everything he needed to only using his eyes.
Some Anvils Need to Be Dropped: Treating people unfairly because they have a different skin color from you is wrong. A similar moral in empathy is dropped with Boo Radley, who is shunned for being different. Remember, the novel was published in 1960; five years before, three white men savagely killed Emmett Till, a 14-year-old black boy, for the "crime" of allegedly flirting at a white woman. The all-white jury acquitted the two killers despite being presented with irrefutable evidence of their guilt after only 30-minutes of deliberation (in fact, the accused then proceeded to boast of their crime in local newspapers, once safe in the protection of Double Jeopardy Laws).
Also Consider The Source. Anyone thinking rationally would take a second look at the accusation of Tom Robinson.
It's hypocritical to defend one group from persecution and then persecute another, as shown when Scout is utterly confused when her teacher talks about how horrible Hitler is for his mistreatment of the Jews, but had cheered on Tom Robinson's death sentence and then insulted the African American community at large. Further underlined when during her lecture on Hitler's persecution of the Jews, a student expresses confusion that he would do such a thing because "They're white, aren't they?" Also, she begins the lesson by pointing out the importance of "Equal rights for all, special rights for none."
Scout's Aunt's church group sneering at the African-Americans while bemoaning how the native Africans live in "sin and squalor" and need to be evangelized.
The book's whole demonstration of the sheer cruelty of the racist attitudes in the Deep South.
Squick: The lines about how long ago Mayella's mother died, and how no one in town is quite sure how many Ewell children there are, could even be taken to imply that the youngest ones are hers.
Tough Act to Follow: Lee avoided this trope by never publishing another book, until 2015. She was often accused of not writing this one (especially since her "childhood friend" was a bestselling author in his own right). People who actually knew Truman Capote dismiss this tinfoil hatting by pointing out he would never have not taken credit for it.
Examined. The teacher Miss Caroline isn't impressed that Scout learned reading at a young age because it goes against the school system. Nowadays she would be skipped ahead a few grades.
This is debateably Values Resonance: while one would like to think that this is an example of wrong-headed thinking long since put aside, in fact it is still sadly common fort children in the American school system to be reprimanded or even punished for being more advanced than the system dictates. Any standardised system is going to let outliers down, and there will always be teachers who act according to the letter rather than the spirit of the education guidelines.
Most Fanfic writers seem to have forgotten that Scout may be a tomboy, but she is also a church-going small-towner from pre-1950s Alabama — many of the things that they have her do in fan fiction (especially fanfic set when Scout is in high school) would give the real Scout a massive attack of the vapours.
Tom Robinson implies that Mayella's father sexually abused her in less than a sentence — one left out of the film note "She says what her pa do to her don't count.", and it is never brought up again, even though Lee wrote the book in the 1960s. This is because it was considered scientific fact that parental incest was imaginary on the part of the child, up until about the '70s. Modern readers, especially high schoolers, are often shocked that this aspect wasn't given greater weight.
Values Resonance: Many of the book's messages and morals are resonant even in today's world. Discrimination against minorities in the US is still widespread, with more attention given nowadays due to the rise of social media platform. While not a focal point of the story, this book does show how damaging false rape accusations really are.
The Woobie: Tom Robinson. He's a nice quiet family man who minded his own business, and occasionally helped Mayella. Nonetheless, Bob Ewell decides to get him killed.
Also, Tom's wife. She does her best to make ends meet for her children after her husband is framed and killed, only to be endlessly harassed by Bob Ewell and considered to be living in "sin and squalor" by the local white women.
Jem qualifies as well. As a kid going through puberty, he already has a lot of difficulties going on, and throughout the book his struggles keep piling up with seeing the reality and how horrifying it truly is and having him and his sister slowly grow apart. May be a Jerkass Woobie given how him growing apart from Scout is somewhat his own fault. He also had genetic heart conditions that gave him an early death.