The film is filled with visual references to 9/11. We see buildings explode and collapse, firetrucks burning in the street, firefighters standing in burning rubble, and of course Batman (seen above) sitting amidst twisted metal, wondering how he failed. And then there's Heath Ledger's Joker, possibly the most interesting on-screen villain of the past decade, standing in for Bin Laden. He's a true supervillain, smarter than his pursuers, able to exploit people's fears to pursue his goals, and totally undeterrable by conventional forms of power.
What does it take to bring down such a villain? As Golda Meir says in "Munich" (2005), "Every civilization finds it necessary to negotiate compromises with its own values." And indeed, Batman must break some rules (including, eventually, the no-kill rule so essential to his identity) to protect Gotham. He famously does so by building a surveillance device that blatantly violates the privacy of every mobile phone user in the city, a device so monstrous that it nearly forces the resignation of his confidante Lucius Fox. This device could serve as a metaphor for the Bush administration's warrantless wiretapping, or "enhanced interrogations," or any other Constitutional violation enacted in order to protect Americans. But Batman rescues his device from abomination by building in important safeguards: it can only be used once, and it can only be used by Fox, the person who despises it most. The device also has the virtue of working -- Batman finds the Joker and brings him to justice. If Bush-era torture had such built-in safeguards, and if it had clearly brought Bin Laden to justice, might we have a different view of it today?
Even this, though, is not enough. Batman is not content with Gotham being protected by a secretive vigilante; if the city's going to ever have hope of being a decent place to live, it will need public servants unafraid to stand in the daylight. So Batman ultimately sacrifices his own reputation to advance what he sees as a necessary lie. He's willing to be the villain himself, loving his city so much that he's willing to be hated by it. This is a decision that no elected official can make -- if you're hated, you're quickly out of power.
The ideas that some truths are too important to be revealed to the people and that sometimes leaders must be despised to do their jobs makes for a rather anti-democratic and complex message. And the film is decidedly ambivalent about how a society of laws should deal with an enemy who appears bound by no laws at all. It also takes on somewhat different meaning today, when our own supervillain has already been caught, killed, and exposed as a sickly middle-aged man sitting in a room full of porn.