For any half-wit with a problem over the flag being at half-staff in honor of Pope John Paul II:
John Paul II was the head of state of another nation, the Vatican City-State. The United States of America has diplomatic relations with the Vatican City-State. We do this out of respect because it is, diplomatically, right and expected. This is a diplomatic issue, not a religious one. If Vladimir Putin were to die a week from now, we'd fly the flag at half-staff for him, too. If we don't make this gesture of respect for the head of state of a nation with whom we have friendly relations, then we send a dangerous message to the entire world.
The French government, which is far more secular and screwed up than our own, did the right thing with their flag and lowered it, and gave this same explanation to their idiot fringe when there were complaints. So, unless you advocate ignoring the rules of national relations and saying that we don't lower our flag for anyone not of our own nation, get a clue and shut up.