The harm would be found in a lack of support for parts of your body (or another person's body) that needs support and doesn't benefit from getting tossed about as you run.
Chafing is another issue, and a lot of runners will wear bandaids over their nipples to prevent bleeding and broken skin. A lot of folks with big legs wear slick shorts that cover at least the tops of their thighs, so that their hip adductors don't rub the skin raw.
Jockstraps have been replaced largely by compression shorts, which for some people (like male Olympic weightlifters) is critical because you really don't want anything sticking out when the bar flies up across your pelvis.
In short, if you can run without the need for protective gear, have fun. People who need support will wear clothes that provide it.