Have you read 1984? The idea of the book is that in the future, the government slowly erodes our rights until one day we wake up and realize that we don't even have the right to think illegal thoughts. Of course, the people are quite safe, but they don't have any freedom, so what's the point?
Your government was founded on principles of civil rights and liberties. One of the rights is to express your ideas and beliefs without fear of persecution. That right is all but gone.
The point of having fundamental rights and freedoms is to protect citizens from the government. The government doesn't exist to control what you think, it's there to make sure everything is working. When the government oversteps its bounds, people should fight back.
The court system is in place to ensure that both government and individual people have the same opportunities to defend themselves. If a court rules that your phone should be tapped for the safety of others, then that's fine. If the court rules that you might be a danger, certain records about you should be released. That's what the courts exist for. But when the government makes an arbitrary, sweeping decision that it wants to see everybody's library books, or everybody's phonecalls, then there's a problem. Ordinary people are being violated without being checked. That's too much power. The shotgun approach is bad, the sniper approach is, potentially, good.
To understand this more fully, picture an evil government. Say for example that Hitler managed to get elected as the US President (he was a very good speaker and politician, after all). There should be no way for him to cause the problems that Hitler caused, your laws and rights and freedoms are in place to protect you from that. If you'll set them aside for a government if you think it's doing the right thing, then it's only a small step to setting them aside for a government that will abuse the powers. That's my major problem with the PATRIOT act -- it gives the government power to act without any kind of safety checks that used to be in place, like requiring a court order to tap a phone. Before a phone is tapped, proper evidence should be obtained, that's just logical.
For more information, see my signature. I added a link this morning to the Wikipedia article on the original version which is about the Nazis. It basically says that if you keep giving up freedoms, even if it's for the supposed good of everybody, eventually they might be coming for you.
<edit> It just occurred to me that the famous question by Juvenal applies here, "Quid custodiet ipsos custodes?" That's a good question to keep in mind when discussing your loss of freedoms for your own "protection".
