On the aspect of religion.

I was in Catholic school in the 1960's, and I can say that where I was at least, they didn't teach anything about a personal relationship with God, in school.

Religion classes were strictly learning the catechism. I was told that I was supposed to figure out a personal relationship with God on my own, without anyone having to tell me. That was told to me by my mom, many years later.

But the Catholic school was very strict, and it would never have occurred to me to think for myself about religion.

Gee Woodle, Space Kadoodle!

I noticed that none of the school employees are praying, and especially Sister Aloysius sort of 'talks around' God. She's fingering her rosary a lot, though. But it's obvious that school rules are more important to her than her vocation - which she only seems to see as a means to have her ways - and also more important than the secret of her own dark sins, of course. That was her fuel to torch the priest (figuratively).
For what reason we will never know. But that's why this is such a great script.
Sister Bitch loses eventually, but not as you would expect. At the end you still don't know anything, yet were handed out quite a few suggestions. And the scene with the mother of the brown boy, it was amazing, almost a movie in itself.
The acting of the three main characters in Doubt is incredibly topnotch. Hoffman, why did you have to die...
I abhor the inhuman Catholic indoctrination (or any other religion), at the same time it also fascinates me to a great extend. That's why I never miss a movie with a christian moral/immoral dilemma theme. This one escaped me in 2008, I recently got the chance to watch it and of course I read the forum threads.
And oh yes, next to Philomena people should see The Magdalena Sisters too. I got SO enjoyably angry there!