I do not know if you are aware of the history, but fanfiction has occasionally been a target of 'cease and desist' motions from various authors/copyright holders. There are certain franchises that you Do Not write fanfic about, or if you do, you do not share it online in any format (not even with a disclaimer). As an example...do not write fanfic about Anne Rice's vampires.
Now, the Tolkien Estate is not one of these bodies. Whether or not they like it, they have allowed fanfiction to exist and have not gone after fanfic writers. IF someone were to try to sell their work, that would be a different matter. The Tolkien Estate goes after fan videos based on Tolkien's work that does not have movie rights (ie, The Silmarillion). Someone tried to make a fan video of the Fall of Gondolin some years back, and that got shut down, hard. There is a reason we have to say that we are not actually making a TV show of the Silmarillion, just talking about a theoretical adaptation!
Basically, this is just a reminder that certain websites have rules like that to protect themselves from any possible repercussions with the copyright holders. If you've ever heard the phrase 'Don't mess with the Mouse', you'll recognize that Disney can come down hard on fan groups who do not comply with the restrictions set down. They are willing to go to great lengths to protect the copyright on their intellectual property, as the current statute of limitations of US copyright law makes very clear. It is no mistake that AO3 (An Archive of Our Own) has a legal team.
So, yes, sometimes a website has to say 'not here, please'. It's not censorship. You're welcome to publish your story on a fanfiction site. ...And that comes to the other point. All internet forums have a focus/purpose, and thus a limitation on what is welcome there. You'll notice we don't exactly have a forum for debating religion and US politics here on Signum U's website - that wouldn't be on topic for anything this site is about. And...apparently, works that are derivative or mention a published work are not welcome on the site you tried to post on. Stuff that is outside the scope is going to be taken down.