Well, I think the issue is two-fold. Firstly, fanfic is almost by definition generally (although not always) less well-written than the original story is. After all, the original story is something that someone managed to get people to buy in reasonably large quantities, whereas fanfic is often written by 13-year-olds with no concept of how to write a story. As a result, OCs also tend to be less good characters than the characters they're placed next to, and thus that sticks out. It's not true of all OCs, of course, but it's true of enough that they get a stigma attached to them.
Secondly, people who are reading a fanfic are doing so because they are interested in the original story, which means the characters, settings etc. OCs aren't part of that, which means they lack the existing connection with the readers that the canon characters have and, therefore, the author has to work harder to get people to be interested in them, and may not be able to do so at all for certain people (I'm not going to be interested in an OC-only story unless the OC happens to have a connection to Sakura, and even then I'd be wary).