That's fine. Some bacteria is actually good for you. Even trace amounts of "bad" bacteria will help build your immune system so you don't need to kill all bacteria.
There's actually pretty good evidence now that childhood sanitation is correlated with the incidence of Acute Lymphoblastic Leukemia (ALL). Edit: accidentally wrote inversely
That's true, but when it comes to hospitals, you want to try and minimize all bacteria. Your skin may be a very protective organ, however if you get those same bacteria in a wound, it could lead to dangerous infection.