Well, magical diseases vary widely in their manifestations, though they are generally either a god/fiend's creation/curse.
More mundane diseases are caused by miasmas - various foul gases trapped in swamps and other fetid places that when occasionally released travel invisibly through the air to be breathed in by the weak-lunged.
As like draws like, these gases tend to settle in other fetid or dirty places, like among the poor of crowded cities, or battlefields strewn with rotting dead.
There is no such thing as germs.