The Dark Knight almost certainly didn't intend to be taken this way, but I found it to be a very humanist-friendly film.
Here we watch a battle between two men who both believe that only Man can decide if the world flourishes or burns. One believes that Man can rise above his chaotic, violent instincts, the other doesn't.
The Joker is an excellent portrayal of the mentality some theists expect to see of atheists. "There is no God, thus, there is no purpose, thus, everything is permitted." He does more than accept and cope with the chaos of the world, he revels in it. More than that, he does everything he can to enhance it so that everyone else will see it and be unable to deny it. No one freaks out if everything goes according to plan, even if the plan is horrifying.
Batman, on the other hand, understands the chaos of the world and has taken it upon himself to help the world cope. He knows his battle can never be won. To paraphrase a prolific comic book writer, Warren Ellis, "The world can neither be perfect or doomed, but it can be better." He understands evil will always return and wreak havoc on the innocent, but we can make incremental progress. We can stubbornly continue to rebuild the sand castle, knowing that the tide of chaos will eventually roll back and smash it to bits. Most, importantly, only we can rebuild that sand castle. Batman is the epitome of one person standing up and deciding to take responsibility, rather than waiting for someone (or something) else to handle it for him. Batman is action, as opposed to prayer.
One man is trying to make the world better, the other is trying to make the world worse. The point is that they both know the choice is theirs. The world is ours to do with as we see fit, and as our natures dictate. There is no cosmic authority to watch over us and decide the results of our actions - they're in our hands.
When we glimpse the pain that chance can inflict on us, will our minds snap like Harvey Dent's? Or will we rise above our anger and put our experience to use, like Bruce Wayne?
When chaos appears, will we devour each other like the gangsters who made a deal with the Joker? Or can we maintain our faith in our fellow men and work to overcome it, like the people trapped in the wired boats?
This was part two of supervillains and religion.