"The air is thick with paranoia in 'Doubt,'...
As its title announces, 'Doubt' isn’t about certainty, but ambiguity, that no man’s land between right and wrong, black and white.
Despite its theological asides and weighty moral stakes, 'Doubt' essentially boils down to a shell game: you think you see the pea under this or that shell, but the prize (answer) remains tauntingly out of reach. So does Father Flynn, a character who for a long stretch appears above reproach: a good, caring, forward-thinking man whose only crime seems to be tolerance.
One of the most eccentric moments in the film occurs when Father Flynn, after admonishing some male students about their dirty fingernails, shows off his long, carefully manicured nails. Mr. Shanley complicates this feeling of gender ambiguity later when Father Flynn, having gone to Sister Aloysius’s office for a meeting, sits behind her desk without asking permission, an assertion of power that opens a fissure in his easygoing facade and says more about the church and gender than any of their increasingly heated exchanges."
-- Manohla Dargis, noticing (again!) how the totem of "tolerance" can be used as a cover for the ugliest of people and deeds, in The New York Times.