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The short answer to this question is that it is difficult to tell. Father Flynn is deceased, of course, in the story, so we are left with second hand memories of the man. It is clear that the story's young narrator was devoted to Flynn, and that the other characters, beginning with Old Cotter and the boy's uncle, have their suspicions of him. "No, I wouldn't say he was exactly...but there was something queer...there was something uncanny about him," Old Cotter says just before the boy learns the priest has died. We never learn exactly what that was, but we do learn that Flynn was a deeply troubled man even before the strokes that incapacitated him. He was never able to forgive himself for breaking a sacramental chalice, and at the end of the story, the priest's sisters describe one very disturbing incident to the boy's aunt:
So one night he was wanted for to go on a call and they couldn't find him anywhere. They looked high up and low down; and still they couldn't see a sight of him anywhere. So then the clerk suggested to try the chapel. So then they got the keys and opened the chapel and the clerk and Father O'Rourke and another priest that was there brought in a light for to look for him…And what do you think but there he was, sitting up by himself in the dark in his confession-box, wide-awake and laughing-like softly to himself?
The reader never discovers exactly what as happened, as Joyce famously ends the story with ellipses after the sister supposes that something had gone terribly wrong. Some of the innuendo, when read alongside Old Cotter's statements about the man, suggests molestation, but Joyce deliberately leaves the issue unresolved. It is thus not clear whether the priest is a malevolent figure, but what is certain is that he was not the self-assured, powerful, authority figure the narrator had believed him to be in life.
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