I agree that sections of the Patriot Act appear to contradict the Constitution. One thing to bear in mind, however, is that the Supreme Court has the power to strike down all or any part of the Patriot Act , if it reviews it , and finds it un-Constitutional. It is the defined purpose of the Judical Branch of the government to interpret the Constition.
The last I checked the Patriot Act was not part of the Constitution, and therefore is subject to the higher authority of the Constitution.
A town I lived in once passed a law stating that a cat owner was responsible for any damage done by his/her cat. However, the State law (Ohio) stated that cats are classified as "feral animals" and thus cannot be "owned" by anyone. So while the local law existed on the books, if anyone ever challenged it, then it would be over-ruled by the higher authority of the State law.
This may be an oversimplification, but I believe the principle is the same in the case of the Patriot Act. What would be best to see, is someone challenging this to the Supreme COurt, but I think that would require some part of the Act to be carried out before someone could challenge its constitutionality.