Operation Enduring Freedom, the Iraq War, the Patriot act, etc, were all based on the premise of defending our freedom, when the reality is Iraq nor Al-Qaeda posed any existential threat to it.

The reason freedoms are often infringed upon in times of crisis are because it is often pragmatic to do so. Also, most of these protestors have little to any idea how the US government works, let alone how its founding father's intended it to. Many would probably be upset at what they read.