It is possible to argue that the Patriot Act has reduced the scopes of these amendments and infringed on American civil liberties.
For example, the First Amendment protects the freedom of association. The Patriot Act makes it illegal to associate with any group that is designated as a terrorist group and it makes it illegal for any person to engage in any action (even if peaceful and legal) that is deemed to support that group. As another example, the act gives the government more power to secretly search people's property. This can be seen as an infringement on or reduction of our 4th Amendment rights against unreasonable searches and seizures.
In these ways, one can at least argue that the Patriot Act has infringed upon our civil liberties.