Explain Like I'm Five

Dogs even not trained by other dogs shake their entire body (like shaking head but entire body) as one of the common ways to express 'im comfortable, good, everything is ok'. When I communicate to my dogs in their language, I often think when doing a shake for 'yes its ok', that this is one of the unusual areas where dog communication and human communication is nearly opposite and I'm curious why. Why does a human shaking their head mean No while a dog doing a similar shake, but of their whole body, translate not explicitly but very closely to Yes?