I am in a position to be far more aware of this fact than most people.
The NSA has been doing this kind of thing for ages; my argument is not specific to that at all. I am arguing against the underlying idea that it is constructive in the long-term to give up civil liberties for the appearance of minor improvements in safety. Losing civil liberties to the government frequently creates at least as many problems for the private citizen as it eliminates, and rarely in a fashion that was envisioned when first implemented.
For example, guns were eliminated from airplanes to keep people safe from "bad guys with guns", though not because so many people actually died from "bad guys with guns". But I guarantee you that 9/11 would have been a much less significant event if we had not eliminated guns from airplanes to make the grass-eaters feel safer from "bad guys with guns". In the final calculus, making people feel "safer" probably needlessly cost many American lives, net. I'll bet there were an awful lot of American citizens on those planes that dearly wished the government would have let them carry a gun on board. Eliminating civil liberties inevitable has negative consequences for life and liberty down the line that the proponents of these "safety measures" never foresaw.
What have we given up in this war? What rights have we lost specifically because of the war?