Life has been rather busy, but I still like to add something to this discussion.
Part of my study was "models of communication". Most simply put: sender - message - receiver.
Now the sender has a "frame of reference", that means his of her background, morals, upbringing, life experience, education, social network, past and present relationships. All of these elements are part of who the sender is.
The same applies to the receiver, he or she also has this frame of reference.
Then we have the message, send to us by the medium (newspaper, letter, radio, television, website). All around there is also "noise", those elements that hinder the message and take away our attention from the message.
In fanfic, you see that the sender reacts to a creation of some one else. The reasons for reacting to this creation like [i]Enterprise[/i] is that the sender relates to Enterprise on a certain level and this reaction has to do with his frame of reference.
I have lived in Japan and studied a couple of languages and I like to play with language, so I have been asked why I don't write about Hoshi, but about T'Pol (and Trip). Now I have been inspired to write about Hoshi due to this site, but first and most I started to write about T'Pol, because I could relate to her: some one who is different than the people around her and keeps her struggles inside and is in love with some very different as well. Hoshi is for me the popular girl in high school, the girl every one likes, T'Pol the one who finds her way, without many friends.
Any way, back to my theory. Like the sender the receiver also has reasons in his of her frame of reference why he likes to read about Enterprise fanfic and why he or she react to certain elements of the story.
Also this frame of reference is the reason why people choose a certain site and how they see this medium. For example, in ff.net most people can post their stories and there isn't an administrator who looks at the quality of the story. This is the reason I don't get upset with misspelling or just shrug when some one writes a character name wrong, but not so on other sites.
There are sites that started because on general sites the lovers of one ship got ridiculed and they were looking for a "safe place" to express their love for a certain ship. Now when a site also has a community, a forum where sender (writer) and receiver (reader) meet, there comes another element into play: the relationship between the people in the community and how they relate to the community. Most simple example of this is that we also tend to read the stories of the person we "know", our friends in the community and also are more willing to comment on their stories, especially when they have commented on yours.
Then we have the noise, sometimes noise can be as simple as the fact that some people are just bad readers. They looked at a story or label from their own perceptive, frame of reference and interpreted that story through their own eyes and sometimes fears, sometimes reading things that aren't there.
To conclude: labels are part of the communication between writer and reader. But like all communication it can be blurred from other things that have little to do with the actual communication (the label) itself.