Let's start by defining our terms. A pedophile is an adult who is sexually attracted to prepubescent children. For those of you just joining us at this blog, I am a pedophile.
People have been putting forward ideas about why we exist for ages. Usually with the idea that if they know our origin, they can get to the business of snuffing us out of existence once and for all. Still, we can't just halt the advancement of human knowledge because genocidal monsters would attempt to make use of it. Better to just recognize that's going to be their intent and press forward with science aware of that risk, in my opinion.
The reason we know as little as we do about pedophilia's origin ties into the fact that there is a vocal minority intent on murdering us in the streets. It's the same reason that the interesting theories on the origin of homosexuality have come about only very recently. Because it's only very recently that homosexuals could participate in such research without putting their lives in danger.
All the current science relating to the origin and nature of pedophilia is hindered by the fact that the samples are heavily biased. Even when researchers take care to utilize phalometric devices in an attempt to confirm that the child molesters they've got in their prison sample are actually attracted to children, they're still dealing with individuals with complicating differences from the general population, and unknown sample biases that will differentiate them from the general prison population outside their sexual response. Of course, that's when the researchers bother to notice that pedophiles and child molesters aren't the same thing, which is not as common as you'd expect for people explicitly conducting research in this area.
Lay psychology using terms like "cycle of abuse" is a particular bad offender in terms of conflating pedophiles with child molesters. One can make an argument for or against "cycle of abuse" as an explanation for some child molesters, but acting as though it has anything to do with the origin of pedophilia is misguided at best. For those of you fond of anecdotes, I'm a pedophile, and was never molested.
Identifying a genetic connection is difficult with current sampling techniques, given all the noise involved with trying to tease out closeted sexual orientations and using prison samples. One of my family members is in prison on child pornography charges (though given what counts as child pornography, no guarantee that has anything to do with pedophilia). Might be coincidence, which is why anecdotes aren't data, but it is enough to make me lean in that direction in the absence of good evidence.
But really, the bottom line is, we'll likely never have good answers as to why pedophiles exist until it's safe enough for us to come out en-mass. At that point, science can get to work doing the research and answering the interesting questions.