It does seem that many people hate clowns, with greater frequency than people hate other things, perhaps eels, for example. But rather than chalk it up to a trendy, pop culture hatred of clowns, I think it might have a deeper source.
Back in my days as an art history student, I remember studying surrealism. One common theme in surrealist art, especially photography, is the depiction of dolls or puppets. The images are often uncomfortable and uncanny, particularly when the dolls are shown in very human-like poses. This coincided with the new (at the time) study of psychoanalysis, which was suggesting that there exists for many people a fear or discomfort with dolls – things that look human, but aren’t. Some of the feelings associated with dolls and puppets are a general suspicion of something that pretends to be human but isn’t, and something that can be seen doing “living” things – walking, sitting, sleeping, or however else you position a doll – but is essentially a dead thing. It is a body without a spirit, yet by manipulating the doll, we can make it mimic human postures and emotions, sometimes with eerie accuracy. Seeing a doll that is mangled or broken evokes a different feeling than a broken tea cup, as it takes the creepy doll thing to a different level. Our first reaction might be to think of it as hurt or injured rather than broken, but how can something that isn’t alive be hurt? The photography of Hans Belmer is a great example of this, and there are scans of his photos at this site: http://eagle.dwc.edu/wellman/Bellmer.htm
So bringing this back to the clown thing, I think many people see clowns as an extension of puppets and dolls. With their costumes and masks (or make-up that functions as a mask), a clown is more like a puppet than a person. A doll can be scary because it is a thing that is masquerading as a person, and a clown is a person masquerading as a thing masquerading as a person. Yikes!
So even though it has earned a spot in pop culture, people have been fascinated or repulsed by clowns for a long time. I would put clowns in the same category as puppets, death masks, zombies, idols, and other things that are human-like without being exactly human. Some people are drawn to this quality, and others are freaked out by it. Some people don’t have much of a reaction at all. It’s not a recent phenomonon, though.