The specific part that is being referenced in the Patriot Act is Article 215, which allows terrorism investigators to view library, business, medical, or other records if they recieve a court's permission to do so, and suspect the person that is being investigated to be involved in a terrorist plot. This requires, again, the Justice Department's permission, and it requires the Justice Department to report to Congress and to all courts precisely how many times it is put into use. To date, Article 215 of the Patriot Act has never been used.
In a post-September 11th world, such a law is necessary. The world will never be the same again. An act such as this has never been brought fourth by any previous Administration of the Executive Branch, but the need for it to exist has always been apparent. Its' creation shows that this Bush Administration is focus on the very real threat of terrorism, and will do everything in its' power to assure the American people that it will not allow it to happen again, under its' watch or under the watch of future Administrations.
Those who deny the need for the Act to exist are reckless, and are a threat to this nation's security.