A few of my thoughts, spoilered for those who haven't seen it.
As a non-Christian (atheistic Buddhist, though I draw inspiration from a wide variety of spiritual traditions, including Christianity), I was gratified to see a film that, while based on a biblical story, wasn't afraid to examine the story from a human perspective, draw from more sources than just the few verses in Genesis and take a look at what the real impact of such a literally world-shattering event would be.
The Watchers, the fallen angels that assist Noah in building the Ark and defend it against Tubal-Cain's army, are based on folktales and esoterica found in both Kaballa and Gnostic sources, and they raise questions on what kind of God would punish his servants for trying to do the right thing. I'm not completely sure, but I think I even heard Noah call one of them Samael, which was Lucifer's original name according to some sources. The notion of angels falling from grace for love of man, rather than from petty jealousy, is a refreshing change from Christianity and American culture's common understanding.
To me, while the most obvious conflict is Noah's guilt over leaving the rest of the world's population to die and his attempts to convince himself that humanity has to end with his family, the most tragic character is actually Tubal Cain. Yes, he is ruthless, evil and cruel, but his scene demanding that God speak to him shows him to be wracked by fear, doubt and yes, guilt. He is evil because he was raised in a dog-eat-dog culture with no room or respect for mercy or kindness, and so he sees such things as weaknesses. In Buddhist understanding, he would be classified as a hungry ghost, forever grasping after what he wants, but never finding any satisfaction in it. Even leaving aside the environmental message, the culture portrayed among the descendants of Cain could easily be a satirical representation of modern America, with a powerful few wielding absolute control over the many's resources and survival.
Noah's struggles with his task and his attempts to convince himself and his family that everyone outside the Ark deserves to die are a refreshingly honest look at what being in a position to decide who lives and dies can do to a person. Imagine every shell-shocked soldier, every guilt-ridden executioner, everyone who's ever killed another in self-defense, and multiply those feelings by millions. It's only natural that he would retreat into misanthropy in an attempt to reconcile his conscience with his actions, convincing himself that he and his family had been chosen for survival from purely practical considerations, rather than any righteousness of their own.
The final explanation for why Ila had twin girls, that God ultimately placed the decision of whether mankind was worth saving in Noah's hands, is a striking and emotional scene because it so closely reflects real life. Every day, we make the decision whether to treat people as equals or objects, as worthy or unworthy of consideration and empathy. In a very real way, this reflects what Jesus said about hate and murder being equal, and while I don't agree that the thought is the same as the action, the thought will always be the seed of the action. Noah's thoughts almost lead him to the action of murder, but ultimately his mind and nature are like the sun: It can be obscured by clouds, but it is always there. He comes to appreciate that there is good in everyone, and it is worth giving them a chance, even if it means feeling that you've failed in something that God has told you to do. It is the story of Abraham and Isaac, but without Abraham's frankly sociopathic dedication to obedience.