In regards smallpox there were multiple strains circulating at any point in time and some were more deadly than others. Which ones spread at any point in time depended on both chance and the particular selection conditions in the population. In populations with high levels of immunity (either natural or acquired) the more mild strains tended to spread, while in populations with low levels of immunity the more lethal strains would tend to spread (lot of complicated reasons for this).

Your general idea is correct though. Just because a disease has been in a population for a long time does not means that it is harmless, not are all new diseases dangerous.