NO DOUBT: TOTAL SPOILER!
The entire movie is peppered with clues and misdirection. Father Flynn is a child molester without doubt. Here are a few points:
1.The screenplay is pretty loaded against Sister Aloysius from the beginning. Her introductory act is to slap the back of a child's head in church. She's presented as the villain. Severe, authoritarian, humorless. We're meant to hate her. Although she takes many redeeming actions throughout the movie, the well is poisoned. In contrast, we like Father Flynn from the get go. He seems charming and open-minded.
2. The idea here is simple. Will we side with a person who we dislike but is right? Or do we side with someone very likeable but who is alleged to be a monster? Since no act of molestation is shown, it's our impulse to believe in Father Flynn because we think he's being demonized. Where's the evidence? How can this 'old bag' be so certain? Innocent until proven guilty and all that. It's much harder to believe in Sister Aloysius. Father Flynn is the easy choice. This is foreshadowed in the first act, 'Ball point pens are the easy way out. Every easy choice today will have its consequences tomorrow.'
3. From the start we're misled into thinking there's a witch-hunt for Father Flynn. When Sister Aloysius hears the sermon about 'Doubt', she bristles. We're meant to think she hates people in the clergy with shaky faith. At the dinner table she asks Sister James if she thinks Father Flynn has doubts. Misdirection towards witch-hunt. In the final scene and not before, we realize why she reacted that way. The sermon resonated with her because of her own doubts. She's not the mindless robot she's made out to be.
4. In the beginning, William London flinches and glares when Father Flynn touches his hand in the courtyard. Father Flynn then insults him in front of his peers making them laugh at his expense. Not very priestly. This is the incident that grabs Sister Aloysius's attention. That's why Sister Aloysius goes into overdrive when Sister James mentions Miller's weird behavior in class after the rectory visit. We're meant to think this is an overreaction based on little evidence, but not if she's already suspicious Flynn made advances on London. This is confirmed in the end when Flynn says goodbye to the congregation, William London smiles to himself. He clearly thinks Flynn's a pervert.
5. Father Flynn also shows that he's an expert manipulator by seeking out Sister James for a chat. He thinks she's the only witness and he wins her over. Like Sister Aloysius says, 'These types are clever.'
6. Father Flynn does show his true character by abusing his power. He threatens that his next sermon will be about 'Intolerance'. And later, from the pulpit he talks very graphically about the effects of 'Gossip'. This is foreshadowed by Sister Aloysius remarking earlier that in Ancient Sparta important matters were decided by who could shout the loudest. And Flynn does shout! He also proves that he doesn't care about his congregation. He flippantly talks about a parishioner and her daughter, calling them both fat. The joke is about their body size and not something the women did. That's mean and petty.
7. Throughout the movie William London and Jimmy Hurley are disrespectful to Father Flynn. This speaks volumes. Also pay attention to the flinch at the basketball court and when they're talking about asking girls to the dance. Shanley is directing our eye by having London be the only kid not wearing a blazer so you notice his mistrusting expression.
8. Our doubt throughout the movie stems from the lack of clear evidence. Because not all is shown to us. Surely, no jury would convict on such flimsy scraps of non-events and hearsay. But if Father Flynn is innocent why does he get a transfer? She can't bully him. The first time they're in her office, he bullies her out of her own chair. He's not scared of her, he's scared because he knows he's been caught. He clearly threatens her with excommunication when he gets nowhere with her by playing the victim card. A sure sign of guilt. He's a sexual predator. They both know it.
9. Sister James says she has sleepless nights because of the doubts. Sister Aloysius says that she should because the predator has gone to an even bigger parish and a bigger school. There is no doubt about Flynn's guilt or his political clout in the church. This shows that Flynn has always been a player.
10. While there are also many other complex themes running through the film, we must remember that there are two battles between Flynn and Aloysius and therefore there are two verdicts. The first one is about selling out tradition for reformation. He is right and she is wrong. Those are her principal doubts. She refers to the changing winds and after talking to Miller's mother she's enveloped by the wind. The second, obviously, is the act of molestation. She is right and he is wrong. Shanley has cleverly written it as one big battle, to cause confusion and doubt within the audience. And both Flynn and Aloysius are on the right side, in one of the battles.