The war on terror is not a war like World War II. The enemy is not a state and it is not clear how victory will be reached. This means any loss of privacy will be open ended and may last for many years.
The USA Patriot Act was signed into law with little debate or congress review only 43 days after the September 11, 2001 terrorist attacks. This article describes some of the pros and cons, and how this Act was created to aid in the War against Terrorists.