US CODE: Title 4, Chapter 1, § 7: Position and manner of display:
(m) The flag, when flown at half-staff, should be first hoisted to the peak for an instant and then lowered to the half-staff position. The flag should be again raised to the peak before it is lowered for the day. On Memorial Day the flag should be displayed at half-staff until noon only, then raised to the top of the staff. By order of the President, the flag shall be flown at half-staff upon the death of principal figures of the United States Government and the Governor of a State, territory, or possession, as a mark of respect to their memory. In the event of the death of other officials or foreign dignitaries, the flag is to be displayed at half-staff according to Presidential instructions or orders, or in accordance with recognized customs or practices not inconsistent with law. In the event of the death of a present or former official of the government of any State, territory, or possession of the United States, the Governor of that State, territory, or possession may proclaim that the National flag shall be flown at half-staff. The flag shall be flown at half-staff 30 days from the death of the President or a former President; 10 days from the day of death of the Vice President, the Chief Justice or a retired Chief Justice of the United States, or the Speaker of the House of Representatives; from the day of death until interment of an Associate Justice of the Supreme Court, a Secretary of an executive or military department, a former Vice President, or the Governor of a State, territory, or possession; and on the day of death and the following day for a Member of Congress. The flag shall be flown at half-staff on Peace Officers Memorial Day, unless that day is also Armed Forces Day. As used in this subsection—
(1) the term “half-staff” means the position of the flag when it is one-half the distance between the top and bottom of the staff;
(2) the term “executive or military department” means any agency listed under sections 101 and 102 of title 5, United States Code; and
(3) the term “Member of Congress” means a Senator, a Representative, a Delegate, or the Resident Commissioner from Puerto Rico.
I personally do not believe that the United States flag should be at half-mast for the pope. He was a good man and all that jazz, but a religious person has never been so honored, have they? What about the seperation of church and state?
Recognizing indeed the importance of seperating church and state, it must also be observed that the Vatican is a sovereign nation (one which many states, including the US, have embassies present). Additionally, the Vatican is recognized by the greater majority of the international community as a sovereign nation (bearing in mind it has observer status within many international organizations, including the United Nations). Because the pope was the leader of his state, will it might hold religious significance for some, if we were not to lower our flags, we would not be acknowledging the death of the leader of a state as is accepted by our national law.