im agnostic and i say bless you too, because it's polite. this is total bs. Did they ban the pledge of allegiance too?
There are petitions to remove "Under God" from it altogether.
But yeah, iirc the phrase "Bless you." originated from Germany or something in the Middle Ages. If you sneezed, it possibly meant that you were coming down with an illness (like the plague or any other of the hundreds of at-the-time deadly diseases), so they'd utter the phrase "Bless you" as a coin of good luck that hopefully you wouldn't pick up something and/or die.