I can sorta see this from both sides. Sure, if you're naked you have large areas of skin exposed to the elements and there will be major heat loss from all of this. But most times we aren't naked - in general we're pretty-well covered up apart from the face/neck/head (and those of us with little hair on top are even more exposed there)! Add to that the fact that - unlike most of our "core" organs that the body protects by reducing bloodflow to other organs - the head is not well-protected by layers of muscle/fat. Or - normally - clothing. The body keeps the blood-lanes open to the head and brain; even though geographically it is an "extremity", the body doesn't regard it as such.
So - yes - in naked form, we'd lose heat - at least initially - based primarily on skin surface area, so the head wouldn't be such a major factor (and is why immersion in cold water can kill so quickly, as all of the body loses heat on soaking). However, in most "normal" situations we aren't naked, apart from the head/hands, and the hands aren't given priority by the body in terms of blood supply. Hence the significantly increased priority afforded the head as - even in extremis - the body will continue to try to pump warm blood to the brain.