Since we are all dumb enough to not know why we're afraid of the dark, it's time to give us a science lesson, eh? It has never been the dark itself that we find so terrifying, it's the fear of whatever monster is hiding in the shadows. This fear is an evolutionary advantage.
We, humans, were always a part of the food chain. Therefore, our great ancestors quickly learned that many predators are sly enough to cover in darkness to hunt. Over time that association strengthened into a subconscious absolute: stay out of the dark because that's where the danger is. This subconscious absolute has been passed down to us -- you might think it's a bad thing, but looking back at it, it's actually a survival skill that can come in handy!
Even if the fear of the dark can manifest itself as an acute reaction, a study conducted at the University of Toronto suggests that the emotion of anxiety plays a specific role in our behavioral responses to stimulation, just as the emotions of love, anger, and sadness do, acting to enlarge our ability to deal with stress and more fully use positive opportunities.
Since that response is connected with natural selection, certain cues more easily invoke the emotion of anxiety and paranoia. This is the result of generation upon generation of early humans reacting to and later preparing for dangers such as these. That's why many ancient threats are more easily instigate a negative response, even in small children, than modern threats do.
While anxiety is deeply rooted in our psychological system, it is not entirely instinctive. We learn fear and anxiety responses from our parents, too. If a small child is frightened of an new or unknown object and its mother responds in a calming manner, the child learns that the item is not a threat. If the parent responds with apprehension herself, though, the child's fears are confirmed and enhanced (that is why we might be afraid of monsters in horror cartoons, movies, etc.). This allows for the offspring to rapidly learn of the dangers around themselves without actually having to experience them.
Not counting all this trouble, it's a pretty beautiful process, eh? This delicate gnawing emotion has been honed and superior over millennia by both nature and nurture into a fundamental survival response that still remains useful in the modern world as it did in the past. Yes, the environmental cues have adapted fairly with the fretfulness over social contacts and property replacing those over finding shelter and not starving to death, although the essential threat response remains: Ensure that you get yours live to replicate one more day. The fear of the dark and the fear of the unknown, are simply there to make sure you don't ever forget it.