The Freakonomics guys are sometimes so determined to be freaky that they are just plain wrong. However, they have this one pretty much right. The Sept. 11, 2001 terrorist attack cost almost 3,000 lives and cost quite a lot of money directly, but by far the greater damage was what we did to ourselves. They point out a lot of costs you probably have thought of and some you haven't thought so much about. But they pass very quickly over the wars in Iraq and Afghanistan, and they say nothing at all about the alienation of our liberties and the perversions of our republic to which most Americans willingly, nay eagerly, acceded.
Juan Cole has a good deal more to say about these deeper costs:
Dick Cheney, Donald Rumsfeld and George W. Bush, however, saw the attacks as “an opportunity.” They were an opportunity to assert American dominance of the oil fields of the Middle East, and therefore, they reasoned, of the energy future of the entire world, ensuring the predominance of the American superpower throughout the twenty-first century. They thus followed a successful overthrow of the Taliban in Afghanistan with a disastrous military occupation of that country. They coddled the military dictatorship of Pervez Musharraf in Pakistan. They threw international law into the trash compactor and invaded and occupied Iraq, kicking off a massive insurgency and then a civil war, and leaving the country a political basket case. They left hundreds of thousands dead and some 4 million displaced. In northern Pakistan and then in Yemen and elsewhere, a covert program of drone strikes was carried out lawlessly and with no oversight; because it is done by the CIA and is classified, our elected officials cannot even confirm that it exists, much less conduct a public debate as to its legality, constitutional validity, or wisdom. . . .
At home, our politicians, bureaucrats and even many judges actively pursued a profound betrayal of the US constitution and its bill of rights, virtually overturning the fourth amendment right to be free of unreasonable search and seizure of private correspondence and effects. Nearly a million Americans were put on a travel watch list and their travel often interfered with, most of them for no reason other than that they had attended peaceful demonstrations. The US government advocated for torture, assassination, and extra-judicial kidnapping. Via Abu Ghraib it became the world’s largest purveyor of prison pornography. A vast and labyrinthine national security state was constructed that appears to be under no one’s control, and the intelligence estimates of which are too numerous and too closely guarded for them ever to be given practical effect by our legislators.
We did this to ourselves. Sept. 11 revealed, not a powerful or even very consequential movement of radical Islamists. Al Qaeda was never anything more than a small, marginal, violent cult. What Sept. 11 revealed is the tragic immaturity of our political culture.