There have been a variety of studies into the phenomenon of clown fear.  Some evidence indicates that having the face covered in paint, thus hiding the genuine appearance and expression contributes to it.  The exaggeration of many clown makeup designs so that just a few facial features are expressed or readable may be part of it.  A lot of clown faces reduce the face to mostly a pair of huge eyes and an extremely large mouth, similar to what primitive man would have seen from predator animals.

Some people don't like how clowns might suddenly play tricks, not knowing whether the clown can be trusted or not.  Although many consider clowns to be entertainment for children, it's kids who often suffer the greatest share of coulrophobia.  And kids who develop a fear of clowns frequently carry that fear over into adulthood undiminished in intensity.

If you suffer from a fear of clowns and you wish you weren't so afraid, there are some things you can do:

See a therapist - There are trained therapists who deal with phobias and if you really have a problem, getting professional help is often one of the best ways to deal with it.

Behavioral therapy - One of the biggest methods used to help people with phobias is behavioral therapy.  Essentially, you start to face your fear in a safe environment with support, so that you can see how the clown won't hurt you.  You might sit down in your living room and look at a picture of a happy clown for a little while.  Then you might move on to watching a movie with circus clowns.  Then you might go somewhere where you can see a balloon clown working.  By slowly exposing yourself to safe clown situations, you can reduce stress and fear around clowns.  If your clown fear is mild, you might be able to do this on your own with a supportive friend holding your hand.  If you really have strong fear, you'll want to work on this sort of thing with a trained therapist.

The best "fear of clowns" story I've heard was told to me and a friend while we were on a road trip in Nevada. In the tiny town of Tonopah is a place called the Clown Motel. We saw their sign while driving by and decided on a whim to stop and see if they had a business card, as their motel sign was so funny.

When we walked into the office/lobby area, we were stunned: the place is FULL of just about everything clown. Clown art, clown stuffed dolls, figurines, you name it. The manager had a nice chat with us and told us about a couple who once stayed at the motel. The husband had been the one to make the reservation. The wife it turned out, had a fear of clowns. The manager couldn't say if the husband knew his wife had a fear of clowns and did it on purpose, or not. Anyway, after this couple checked in to their room, the wife came back to the motel office, asking if there was any way she could have the clown art removed from the walls of their room. The art is permanently affixed to the walls so it can't be stolen. The manager was really surprised that this lady wanted to take down the clowns and said to her, "Hey, it's the CLOWN MOTEL! What did you expect?"