I find it funny that there's a bigger uproar against airport security screenings than there is against a war where civilians are injured and killed. Both are related to terror, but what a difference in perception.
In the case of airport screenings, it's pretty clear that cost >> benefit. Cost = sleazy govt employee looking/touching at my balls, and maybe saving the photos. Benefit = risk of death reduced by an amount less than 1 extra gym session per year.
In the case of the assorted wars, it's not as clear. Cost = visible casualties of real war in Afghanistan. Benefit = preventing the invisible casualties of 10-15 years more living under the Taliban + invisible civil wars that would have eventually overthrown the Taliban.
(Fun fact: on 9/12 or 9/13, shortly after Osama was labelled as the culprit, an Afghani friend IMed me. "I'm very sorry for what happened to your country, but this could be the greatest thing that ever happened to mine." He then expressed a hope that we wouldn't "pull a somalia".)
His general perspective was that you have war/tyranny regardless of US involvement, but at least with US involvement there is hope for the future. He was also pretty critical of western anti-war types - he thought they cared more not seeing war on TV than actually about the actual victims of war/tyranny.
(Note: his perspective was a little unusual by Afghani standards. He wasn't Muslim and only part of his family escaped to US (in 1996) on refugee visas, fleeing persecution. )
You're probably correct that there should be greater public outcry over civilian casualties in war, but that doesn't mean we can't rally against privacy-invading things like full body scanners.
On the other hand, most people would be bothered if I touched their balls or viewed nude pictures of them on my computer.
Apparently some people feel similarly about homeland security doing these things.
I think part of the reason for the lack of outrage over The Patriot Act was the timing. When the Patriot Act was created, it was a short enough time after 9/11 that the US was still strongly emotionally effected by it. It was easier to say "This will prevent terrorism" and be believed.
Years later, it's become easier to take a rational look at the risks and benefits, and see that it's unlikely that such measures will prevent enough terrorism to outweigh the costs.