First of all, let me say it is very natural for a writer to put herself/himself into a story. I would doubt the veracity of any writer who claimed that they had never done it. Pro writers do it all the time. They, of course, do it very well. They are also dealing with all original characters so they can put in anyone they chose. In fan fiction, we are playing in a world created by others. It is a world that other people know and love as much as the writer does, therefore the options are more limited. A true Mary Sue is basically wish fulfillment. It is lots of fun to write yourself in and get the guy you want. It is even a fairly good learning tool and fun to share among intimate friends. It is not, however, what everybody else wants to read. We all have our own fantasies where we get the guy, so we resent your Mary Sue for doing it.
As a reader, if I pick up a story and it is two or three paragraphs about a character I don't know I have pretty much lost interest. Generally the lead character is the one that the story revolves around and quite frankly, I read fan fiction for the characters I know and love and not any other. Those are my feelings as a reader. As an editor I can get past that because I know that my feelings do not reflect those of all my readers. There have been some very popular original characters over the years.
There is a pretty hard and fast rule in series television that the only strong guest star character must be the villain and that any love interest must be killed off during the show. The reason for that is that a strong good guy needs a strong bad guy to give him purpose and showcase his talents and a love interest changes the character too much. Both of these are true and apply to fan fiction as well. Look how many TV shows have disappeared once the hero was ‘settled down'. The whole premise had changed and usually the show suffered for it. In most cases, this holds true for fan fiction also. I say most cases because there are some fans who do like to see the hero in that position. However, even in that case, it takes an exceptional writer to carry this off.
Does this mean there can be no female characters or heaven forbid, strong female characters? Absolutely not! All female characters are not Mary Sues. Some of Mary Sue's attributes include -- beauty, wealth, talent, extreme intelligence and the only point of her being in the story is to get the guy. Mary Sue can either rescue the hero or be rescued by him but, in any case, she overshadows everyone else in the cast with the possible exception of her guy and he generally plays second fiddle to her also. The real plot in any of her stories is how she can get the guy. If your character has a purpose in the story that actually advances the plot then there is a good chance that she is not a Mary Sue and does belong there. Even if that is the case, if you can not write a story in your fandom that does not include this character you may be obsessed with her and should try writing a few without her just to be sure. A recurring character in a minor role is far more acceptable than a "co-star."
The reason long time fan fiction readers hate Mary Sue is because we have been inundated with her for over thirty years. We all have our own and if we want to read about any Mary Sue it will be the ones we created ourselves. Keep Mary Sue among friends but use the techniques you learn from writing Mary Sue stories to turn out the kind of fan fiction everybody wants to read. Make your female characters strong and believable and most of all, make them people in their own right -- not groupies or bimbos. Women who are only complete when they have a man are boring in real life and boring in fiction. If you are going to create a character, make it one worthy of everyone's effort. And don't worry if a little part of you creeps into your character just make it the part that makes you what you are, not what you might like to be. We'll probably like you a whole lot more than we would Mary Sue.
Good luck!
BTW -- If you think that I'm just a crabby old bat (well, I am but that's besides the point) and I am alone in my hatred Mary Sue, check out this site which is a spoof of Mary Sue and includes a collection similar essays written by other experienced fan fiction writers. Bottom line is Mary Sue is a big bore and NO ONE wants to read about her.