My answer is in your question. How do you know the government isn't lying or mistaken? Our system says that the burden of proof in a criminal case is on the government. We simply cannot let go of that protection or we are all subject to arrest any time without any wrong doing on our part. If you think that you are happy trusting Bush and Ashcroft not to misuse it, think about some time in the future when maybe Hillary is president. What will stop her from deciding that FReepers are enemy combatants?
What Patriot Act provisions do you have a problem with?
If you want one key point it is that the warrants that are required in some circumstances are no longer issued on probable cause only. The standard is now-"the government wants a warrant". Recent additions have eliminated even this for some financial inquiries.
Jose Padilla is not being accused as a "criminal." He is being held as a combatant - part of the 'army' of terrorists who are sworn to maim and kill Americans in America. He was not just "met by the FBI" at O'Hare airport on a whim. His every movement from Pakistan to the US was under surveillance.
I bet you know all of this but just 'feel' good about your libertarian 'principles.'
What part of "war" do you not want to understand?