The saying God Bless you after a person sneezes is believed to originated in the early days when the bubonic plague was ravaging Europe in Rome.
With the bubonic plague sneezing was one of the symptoms associated with it.
Pope Gregory I suggested that a tiny prayer in the form of saying the words and prayer "God Bless You" after a sneeze would protect the person suffering from bubonic plague from death.
It's basically a small prayer to say god bless you to someone after a sneeze even though just sneezing without any other illness will not be deadly.
It's still just stuck in most peoples heads today to just say god bless you after someone sneezes.