"The pills Dr. Mario throws to destroy the viruses are in fact the major threat. The viruses in the bottle can never actually do any harm. In fact, it is the pills that can do harm, causing the player to lose the game if they obstruct the neck of the bottle. Thus Dr. Mario is, as a game, one about bad medicine."
Remember that Italian plumber/garbage man whose primary experience is in the field of Gorilla Rape Victim Rescuer? Well, he somehow earned a medical degree (it's best not to ask where), and he wants to treat your diseases by throwing every conceivable kind of medication at them until they explode.
"Brightly colored pills! They'll cure all your ills! Just as long as you've got fever or the chills!"