As has been said, the fear of darkness comes from the fact that it's much harder to see what's in it. It's not the dark, it's what's in the dark, or what you might think is in the dark. If you couple that with an inherit paranoia your mind can really play tricks on you. Then there's the legitimate feeling of walking around in the woods at night by yourself and seeing a mountain lion 40 yards in front of you and watching it walk off into the dark and being scared. I still live in one of those rare areas where you can drive for 20 minutes and be out of the city and into heavy woods, that's when not being able to see around you at night gets creepy. Mountain lions, coyotes, and wolves, oh my. I'd say it's an evolutionary trait, for almost 200,000 years mankind existed without any really reliable light sources. If you went out in the dark, you had to be scared because our night vision is very limited compared to predatory animals. Fear of the dark was basically bred into us for our protection.
In my house I'm not afraid of the dark, when I go for a walk at night I'm not quite scared but nervous and cautious enough, seeing four inch diameter cat prints half a mile from your house does that.