The Fourth Amendment applies only to areas where citizens have a reasonable expectation of privacy. The Court held in a landmark case of Katz in the 1960s that there exists a reasonable expectation of privacy in the contents of a phone call from a public phone booth, and therefore the government's use of the conversation without a warrant or probable cause was improper, and therefore any conviction of Mr. Katz, based on illegally obtained information, had to be thrown out.
However, while the expectation of privacy exists in the actual phone conversation, there is no such expectation in the fact that the call was placed at a specific time from a specific place. The conversation used a third party (the phone company), which lessens the expaectation of privacy on the basis that a call was made.
I have always had problems with some of the provisions of the Patriot Act, and I believe taht some of the provisions, like roving wiretaps and surveillaance of any private call between people in the US and a foreign country, when challenged, will be deemed unconstitutional.
I found it ironic that Bush had claimed after 9/11 that the attackers disliked us because of our freedoms, but the government responded by enacting legislation that curtailed freedoms. Obviousy the American government distrusts the people it represents as much as the people distrust it.
I never thought of your last point, on freedoms. Makes one think differently about it. We have lost privacy since then, for certain.