I think it's based on a tradition in some African country (I think Nigeria, but I may be wrong) where women show men their nakedness as a way to shame them. I read about this recently where some women intended to protest at a factory that way. The idea being that if men saw their mothers and other women of standing in the community naked, they would be so overcome with shame that they would do anything to avoid that.
The naked protesters here in America adopted the idea... show their nakedness as a way to shame people into stopping the war.
I can never figure out what protesting naked has to do with anything.