The biggest flying/airport outrages are a lack of markets in allocating scarce resources, and the resulting unacceptable airport and flight delay problems in places such as JFK and LaGuardia. Next come airlines which ruthlessly screw you over, repeatedly, and lie to you and mistreat you. I do understand the trade-off and prefer the lower prices and fewer quality assurances; still, you can object to their behavior at the margin — it's often unethical. Let's get worked up over these problems first.
I view good scans as, in the long run, a substitute for patdowns. One option is to have very very good scans, nude "photos," fewer patdowns, and to have Americans shift to a more European attitude on nude bodies. There's even an available status attitude where you don't mind or notice the scans, much as the King allowed himself to be dressed and handled by commoners. That's the intelligent argument for the current shift in policy. Maybe the enhanced scans simply aren't useful or maybe Americans can't or won't shift their norms. Those would be reasons not to do it (and I am not pronouncing a definitive opinion here) but it's simply not, in principle, that objectionable of a policy. There's a locked-in structure which prevents a competitive test of safety levels and so all alternatives are coercive in some manner, including the difficulty any airline would face in attempting an even more restrictive set of security procedures.
It's worth asking how intrusive a search markets would provide, but keep in mind there are significant negative externalities from exploding airplanes and also there are government bailouts which limit the downside. Furthermore companies do not always care enough about "extreme negative skewness," as we have learned in financial markets and thus there is a case for regulating a tougher security standard.
Hovering in the background is the reality that a few successful downings will kill many people and furthermore probably wipe out the insurance market and thus lead to nationalization of the airlines. It's not clear what the freedom-enhancing path looks like and there is no default setting of market accountability. It's "elephant interventions" all the way down.
It's worth comparing the current American response to earlier British crises (IRA troubles, and eventual CCTV) or for that matter Israeli responses to Palestinian suicide bombings. In these kinds of situations something has to give — usually by public demand for better outcomes more than a state usurpation of power.
I would not say that "we are now at war with the terrorists" but our situation has some war-like elements. Any persistent war has required major social changes, if only temporary ones, in how the body is viewed and handled. If we are so unwilling to even consider these changes in body viewing norms, I wonder how we will respond when scarier events happen, as they likely will.
The funny thing is this: when Americans insist on total liberty against external molestation, it motivates both good responses and bad ones. It supports a libertarian desire for freedom against government abuse, but the same sentiments generate a lot of anti-liberal policies when it comes to immigration, foreign policy, torture, rendition, attitudes toward Muslims, executive power, and most generally treatment of "others." An insistence on zero molestation, zero risk, isn't as pro-liberty as it appears in the isolated context of pat-downs. It leads us to impose a lot of costs on others, usually without thinking much about their rights.
The issue reminds me of the taxation and spending debates; many Americans want low taxes and high government spending, forever. For airline security, at times we want to treat it as a matter of mere law enforcement, to be handled by others, and one which should not inconvenience our daily lives or infringe on our rights. At the same time, so many Americans view airline security as a vital matter of foreign policy and indeed as part of a war. We own and promote this view and yet we are outraged when asked to behave as one might be expected to in a theater of war.
The main danger to liberty here is not the TSA but rather a set of American attitudes which, at the same time, take our current "war" both far too seriously and also not nearly seriously enough.
Overall, I'd like to see less posturing in these debates and more Thucydides.