I think when it's concerning fanfiction related to manga, these disturbing theme (incest, rape etc) exist because unfortunately the manga's world DOES frequently contain these themes.
As much as I LOVE mangas and the Japanese culture, I have been forced to realise that the Japanese taste in terms of litterature can sometimes quite....disturbing. Or maybe they are more honest about it? They are open about liking incest/rapes/torture/ - and express these tates without any inhibitions in their litterature.
The past year I have (finally) started to read other mangas than Naruto / Bleach / One Piece(the nicey adventurous types) etc, and trust me, the fanfictions mentioned here is much more TAME as some of the mangas that I have come accross! And I'm talking about very easily accessible mangas, as accessible as Naruto etc and present in all manga sites. But read them did I, out of (morbid) curiosity- gritting my teeth and holding my horrifying heart to be able to go through some of them and sometimes just could not.
So, what I'm trying to say is that the people who actually wrote these disturbing fanfictions mentioned above maybe be those who are used to those types of mangas too.
Madz