omg great question! back in the day when the bubonic plague, or "Black Death" was going around, a sneeze would indicate that the person was infected and soon would die so people started saying God Bless You, as a way of saying may god have mercy over your soul or a farewell.
The exact reason why people say "Bless you" after you sneeze is quite historic. It is coined from the phrase "God bless you", that is attributed to Pope Gregory the Great, who uttered it in the sixth century during a bubonic plague epidemic. Today people use it as a polite gesture when someone sneezes.