The Atlantic Magazine website has a short, but interesting, article on Clowns and why they're often considered frightening.
Traditionally clowns are anarchic figures who defy the boundaries of normal social conduct, even before Heath Ledger's Joker just wanted to watch the world burn. In Edgar Allan Poe's 1849 story Hop-Frog, a physically deformed court jester who's consistently the butt of practical jokes encourages the king and his court of noblemen to dress as orangutans covered in tar, at which point he sets them all on fire. The unpredictable nature of a clown's behavior, and his or her tendency to transgress acceptable standards of behavior (by, for example, throwing pies in each others' faces, or squirting water on an innocent bystander with a trick buttonhole flower), probably makes us wary of what other lines they might cross.
Is it the makeup, the clothes, John Wayne Gacy, whatever the root cause, we're sure Clowns are going to be scaring people for a long time.
Check out our previous post about clowns here.