Whenever I'm in class and I sneeze, about eight people around me clamor to say "Bless you," that ridiculous nonsensical thing you're supposed to say to be polite. This really grinds my gears.
First of all, I think everyone agrees that the actual words of the phrase have no meaning. I don't think there's anyone who seriously believes that your soul is escaping when you sneeze and that saying "Bless you," crams it back in. Everyone understands that it is just an antiquated little phrase from a time long past. But everyone says it anyway, because they think it's polite. And here we hit the crux of the problem.
We should be polite because it demonstrates respect for the people around you. Saying please, thank you, that sort of thing is respectful more than anything else. That's why we do it. But saying "Bless you," after a sneeze is anything but respectful. In fact, it's kind of rude to point out and acknowledge someone else's bodily functions like that. I've read Miss Manners, and the rule of thumb is to ignore people's bodily functions. Pretend they didn't happen. That is polite and respectful.
Except when it comes to sneezes, when you're supposed to robotically spout this nonsense phrase. Why don't we do that for any other bodily function? There's no dumb little phrase you're supposed to say in response to someone's cough or fart or throat clear. There's no reason why sneezing should be any different.