In your bloggers most humble opinion the root cause of this "phobia" is the grease-paint and prostheses that clowns traditionally adopt to create exaggerated features and facial expressions. Humans often find false facial expressions "creepy".
Although for some people (such as your humble blogger) false or extremely exaggerated expressions may appear more comical than creepy. Your blogger must admit that he has never suffered from coulrophobia, and as a child, was not adverse to reading sci-fi and horror, and not phobic about snakes, spiders or creepy-crawlie things
What one person may find creepy, another may find fascinating or amusing. Although, one of the things that many people do find a little "creepy" are (modern) CGI depictions of human characters. And that's because they are too realistic. ... Early attempts at CGI were easy for most people to cope with. The depictions were obviously computer generated and audiences had no problem with them. However the number of computations involved in creating the images has grown exponentially and these have become increasingly realistic. Modern CGI creations can have realistic beads of sweat, hair that ripples precisely in the wind, facial muscles and eye movements that give an accurate simulation of human emotions ... And yet the finely tuned human eyes of the audience detect something wrong. And hence the CGI creations appear "creepy" ... Your blogger would hazard a guess that this why CGI characters have mainly been confined to "The Genre" (whatever that means these days).
The above also has implications for synthetic humans (androids).
Nevertheless there are many children (and adults) who find (the obviously exaggerated features of) clowns disturbing and/or frightening. And this unease has been pumped up by pop culture. The Epitome of the killer clown would be Stephen King's IT and the DC comic character, The Joker ... And of course Heath Ledger deserves an honourable mention here. His depiction of the ultimate killer clown has been immortalised by his premature death. The current wave of scary clowns is tapping into this rich vein of pop culture and modern urban folklore. And as such your blogger must opine that it is, at best, an ill-advised prank that has the potential to backfire with tragic consequences for both the perpetrator(s) and intended victim(s).
The current "fear of clowns" story, which has been doing the rounds in Australia has been pumped up even further by the media. This was all summed up neatly in the ABC program "Media Watch" on Monday night, as mostly due to lazy journalists recycling videos from the Internet without doing even basic fact checking
Although, when discussing scary clowns, it's difficult to avoid mentioning Donald Trump in the very next if not the same sentence ... It's certainly uppermost in the minds of folks in the social media realm ... And would it be cruel but fair for your blogger to suggest that it is and will continue to back-fire for "The Donald"? Try googling for "Donald Trump scary clown" and you'll find over a million matches. We might conclude therefore that the current Scary Clown phenomenom will end sometime after November the 8th, 2016 (Or maybe it will get worse if US voters don't pull back from brink?)
There is an associated theme that deserves a mention ... And this is unease about children and things associated with children. Horror themes that develop along these lines will take the seemingly innocent child or the games that children play and present them as sinister or menacing. In this regard, Stephen King, the old master of modern fears, delivers many examples in his first short story collection (Nightshift) and of course novels such as "Fire Starter", "The Shining" etc. It is another interesting theme and not the same as pedophobia, because it is not so much the fear of children and/or infants as the feeling that there may be something (inherently) sinister about them. If could be a misogynistic association of children and motherhood, or it could be an association with "original sin" (i.e. we are all fundamentally flawed and children especially because they are closer to the fundamental human nature --- whatever that may be).