If memory serves, it stems from plague-ridden times where if someone sneezed, obviously they had or were contracting the plague, so a quick "bless you" before they died would be quite welcome.
Nowadays, with modern medicine, plagues aren't as prevalent and diversity renders a "bless you" a throwaway phrase that's potentially offensive.
First of all, you don't mean it, but you feel compelled to say it. It's a socially expected, sort of habitual Tourette syndrome. If you truly WANT to express vocal concern for a sneezer's wellbeing, personalize it, and don't tack any sort of religious meaning to it -- Because, secondly, are you a priest - priestess - shaman - monk - warlock - friar - nun - witch - etc.? And do we attend the same rituals? Your unthinking blessing could be received as well as holy water to a wampyr - and that means you're crossing the line.
As I type this, my neighbor just sneezed! (How timely.) And I sit here thinking "I really should say something." "Must . . . acknowledge . . . sneeze."
Why do I feel this? It is purely only habit and tradition. But NO MORE! I'm going to break the pointless cycle and ignore the sneeze.
Now, when I sneeze, I'm sure I will experience a thoughtless blessing. What should I do?
God bless you.
AAAAAGGHHH ! IT BURNS ! WHAT HAVE YOU DONE !? I'LL GET YOU FOR THIS !