A number of years ago, I heard someone (George Carlin maybe? Commenters help!) ask "What's the worst thing that can happen to you if you smoke pot" and the answer was "Get thrown in jail". The not so subtle message was that the preventative measures applied to prevent marijuana use were worse than the drug use itself.
I would say this fairly summarizes my fears about government responses post 9/11. Reason's Hit and Run quotes T.J. Rogers along the same lines:
What's the worst thing that Al-Qaida can do to America? We have
probably already seen it. Of course, the government can talk about
bigger things, like the use of weapons of mass destruction, to justify
its use of totalitarian tactics.
I would much rather live as a free man under the highly improbable
threat of another significant Al-Qaida attack than I would as a serf,
spied on by an oppressive government that can jail me secretly, without
charges. If the Patriot Act defines the term "patriot," then I am
certainly not one.
By far, our own government is a bigger threat to our freedom than any possible menace posed by Al-Qaida.
The worst thing the terrorists can do is not another 9/11, but to push America into abandoning its separation of powers and its traditional protections of individual rights.
Reasonable people can disagree whether the Patriot Act goes too far in violating civil rights. I personally opposed most of the measures in that act when Bill Clinton proposed them the first time and opposed them again this time around. However, whether I support the Act or not, at least the Act and its provisions are still following the separation of powers script written into our country's DNA: Congress proposes new administrative powers vis a vis searches, the administration and justice organizations follow the procedures, with certain oversight and appeals rights granted to the courts.
What worries me more than the Patriot Act is the administration's claiming of broader and broader police state powers in the name of combatting terrorism, whether it be detaining people indefinitely without a warrant or eavesdropping on citizens without a warrant. I understand that both of these programs have practical goals related to security, but I think that most of these goals can still be reached by continuing to respects separation of powers. Congress must still set the rules for a program such as detention of suspected enemy combatants, and these rules should include a role for the judiciary to review individual cases.