By skyforbes The script is deliberately ambiguous but John Patrick Shanley, the writer, informed the actors who played Flynn in both the play and the film of whether he was guilty or not. Meryl Streep, therefore, did not actually know herself.
He's certainly hiding something. But perhaps he left his old parish following an affair with an adult parishioner. Unethical perhaps, but not even close to the level of vile of what Aloysius accused him of having done.
Plus, Aloysius says at the end that she has doubts. But is she referring to his guilt? Or maybe she was certain but now isn't. She had a vendetta against him due to him being too modern, after all. Perhaps she was blinded and reconsidered too late. She was shown to be a hypocrite, after all.
Or perhaps she was referring not to Flynn at all, but her faith in God.
What do you think?