In the end, this becomes the critical element of Doubt. Simply put, we don't know. When Sister Aloysius confesses at the end that all she really has is "doubt," it is a reflection of how "evidence" is something that can be doubted and debated. Much of one's view depends on a personal view of the situation. If one is predisposed to think that Father Flynn did infringe on Donald's rights, then they would be persuaded by the same elements that compelled Sister Aloysius. Items such as the "history" at other schools, the excessive concern that is present between Father Flynn and the boy, as well as the fact that Father Flynn acquiesces to the Sister's threats could all be seen as evidence of guilt. Yet, one could be equally valid in suggesting that none of this is "hard" and valid evidence.
In the end, what the sister presences is not conclusive. It is perception based, which, by definition, makes it far from conclusive. This is the root of "doubt." In the end, Sister Aloysius and all of us are left with more doubt than anything else. This becomes the only conclusive certainty.