I watched Doubt assuming I knew the storyline: a repressive, reactionary Church caused the sex abuse scandal. Surprisingly, that is not what it turned out to be. I think this post from First Thoughts has it right for the most part.
Here are my few quibbles. He read the set of scenes contrasting the Nuns and Priests as Pious v. Impious. I read it as Women v. Men i.e. making a feminist point. Also, he read the last scene and the Nun’s doubt to be about the hierarchy while I understood it to be about her decision to lie in order to serve God. She repeats a line she had said earlier, "Sometimes, one has to take a step away from God in order to serve him."
On another note, the film seems to be misnamed. The screenwriter said he had come up with the title first and the story later. This makes sense since the theme of doubt v. certainty is a secondary matter. What appears to be primary is the theme of simplicity v. complexity. Amy Adams’ character “wants simplicity back.” The characters you expect to be good are bad and vice versa.