John Patrick Shanley's Doubt is not a play about the relative merits of child molesting or kindness but about that terrible feeling that one does not know the right course. The two main characters, Sister Aloysius and Father Flynn, are each

        The Church is an environment that encourages security, an environment wherein the uncertainty that rules the outside world is minimized, if not overcome. Some additional key elements of Doubt are the issue of certainty, compassion, vulnerability, doubt, and how difficult it is, even in an environment of faith.

        John Patrick Shanley uses the word "doubt" in two specific, deliberate places, defining the extremism of the two main characters. Early on, before we have even been made aware of Sister Aloysius's suspicions of Father Flynn, the subject of his possibly having a shameful secret is raised when Sister Aloysius and Sister James are discussing his latest sermon, on the topic of Doubt.  Sister Aloysius wonders in a provocative way, "Is Father Flynn in Doubt, is he concerned that someone else is in Doubt?" Much later, when her allegations of sexual abuse become apparent, this question makes sense; outside the context of his crime, however, it seems that Sister Aloysius, who is stringent in her ways, looks down on the priest only because he lacks absolute certainty. At the end of the story, though, having won a battle of wills over Father Flynn, Sister Aloysius suffers from her own uncertainty. "I have doubts!" she exclaims to Sister James. "I have such doubts!" If certainty is what allows Father Flynn to continue as a child molester without crumbling under a guilty conscience and what allows Sister Aloysius to pursue a possibly innocent man, then uncertainty in the play is not presented as being any more attractive.  Father Flynn's history is with the Church, and, so far at least, it has been a successful one. If Sister Aloysius is right (and her successful bluff at the end indicates that she probably is), Father Flynn has behaved criminally before and beaten the rap, and so there is no reason to expect that he will not do so again. Perhaps he really does believe that his sexual relations with children are based in love, but, at some level at least, he knows that there is nowhere but the Church where such behavior would be protected. His past is within the Church, his future is within the Church, and in neither past nor future does his behavior earn him the sort of punishment that it would in the real world.

        Father Flynn is a caring man who tries to break down the social barriers that separate him from the boys in his class. His compassion is conscious, a trait that he actively pursues, believing that it is more important for the boys to feel loved than it is for them to be pressured by rules. In particular, he makes a point of giving extra attention to Donald Muller because he feels that the boy can use a friend, given his circumstances. His extraordinary friendship with the boy is suspicious, if not inappropriate. Even if he is not, as Sister Aloysius assumes, sexually involved with the boy, Father Flynn's desire to ignore common social boundaries puts him in a position that threatens his career. By traditional dramatic standards, his need for acceptance can be seen as a tragic flaw in that it is a character trait that leads to his downfall.

        Compassion is not generally viewed as a flaw.  Sister Aloysius characterizes innocence in teachers as self-indulgent and lazy by discussing the teaching style of Sister James,. To her, a teacher who tries to befriend a student is doing so for selfish reasons. As much as Father Flynn is adamant in his insistence that children should be treated with compassion, Sister Aloysius is adamant that such ideas are a sign of impure intentions. Whether or not he is a sexual predator, Father Flynn draws attention to himself with his insistence on behaving as the boys' friend.

        Father Flynn is just as certain that he himself is a force for good and that, with his emphasis on love and compassion, he is better for the boys than Sister Aloysius is. In the end, his retreat from St. Nicholas seems to be an admission of guilt, but he never verbally acknowledges having done wrong. Father Flynn comes from a working-class background, and he is comfortable with the boys of his parish. He teaches religion and physical education. His manner with the boys, is tough yet caring: he offers advice; criticizes; pokes fun; and, in the end, invites them back to the rectory with him for Kool-Aid and cookies. When he is accused of giving Donald Muller wine as a way to approach him for sexual favors, he explains that he was really protecting Donald from being thrown out of school after he found out the boy had drunk some of the altar wine. Father Flynn tells Sister James that he believes in being open and caring, that he follows the Bible's teachings of love.

        Sister Aloysius is certain that there is sexual abuse going on at St. Nicholas, even before she has any substantial proof of it. She says late in the play that her certainty grew from one small gesture: the way in which one of the students recoiled from Father Flynn's touch. The evidence that she compiles as a result is flimsy and easily explained away. She takes such minor issues as the length of Father Flynn's fingernails and the fact that he lectures the boys on being men to be support of her suspicion. When Father Flynn offers reasonable explanations for his behavior, she persists. He believes that her personal dislike for his teaching style may be strengthening her sense of certainty. She is even willing to threaten trouble for the boy, who presumably is the victim in this case. She shows no sense of uncertainty until the play's last line, when she admits to having doubts.

        There are two characters in Doubt who are used to represent vulnerability. The first and most obvious is Donald Muller, the student who is suspected of having been sexually abused. Donald has recently transferred from another school and is the first black student to attend St. Nicholas. When she hears that Father Flynn has established himself as a "protector" to Donald, Sister Aloysius immediately assumes that his motive is to take advantage of him. "He's isolated," she explains to Sister James. "The little sheep lagging behind is the one the wolf goes for." While the teachers who advocate compassion—Sister James and Father Flynn—see Donald's vulnerability as a responsibility, Sister Aloysius has no doubt that an unscrupulous predator will take advantage of any weakness.

        Sister Aloysius and Father Flynn, each hold staunchly to their views of the world and are unwilling to see things as others do: this unwillingness to yield is both a strength and a weakness and leads to the final tragic conclusion. The other two characters, Sister James and Mrs. Muller, are racked with doubt, areb able to see both sides of their dilemma.