Laurie Mylroie writes in National Review on some of the problems and absurdities the government (specifically our law-enforcement agencies) must go through to protect us from terrorism - Mishandling Terrorism: The law-enforcement mistake.

Mylroie gets into some of the specifics of the dangers of treating terror as a law enforcement issue, and more specifically "The Wall" put up between criminal and terror investigations and how this wall makes it more than just troublesome for our enforcement and investigative agencies.

After Mylroie's piece, you might want to check out this lengthy article by Heather Mac Donald, Why the FBI Didn't Stop 9/11 (Thanks to Mal in the comments with a timely pointer.). It gets into many of the same issues and then some, and in even more depth. Don't let the length turn you off, it's worth it.

Then, you can go back and review this concise Slate four part series on understanding the USA Patriot Act with a renewed depth of understanding of some of the important issues involved. There are no doubt still sections of the act to be concerned with, but concern is one thing, hysteria another, and unfortunately there's a lot of the latter floating around out there these days. The blathering of pundits and political hacks is no substitute for some of the nitty-gritty specifics elucidated in the first two articles. Highly recommended.