Fanfiction also is generally structurally different.
If you want to write a novel, you are kept to a pretty strict word range--generally 70-120k words, though that varies a bit up or down depending on the genre. Some genres have fairly strict structural and plot expectations, as well.
A romance novel is a specific thing. A mystery novel is a specific thing. Being able to write a shippy fanfic, even one of the correct length to count as a romance novel, does not necessarily mean that you know how to write a romance novel--because there are different expectations between them.
Fanfiction is often in conversation with other fanfiction, and published fiction is often to varying degrees in conversation with other published fiction--but despite what a lot of people seem to think, published fiction is often not actually in conversation with fanfiction, even if fanfiction is in conversation with published fiction.
One thing that you tend to see with people writing original fiction for publication who don't really read much published fiction in that genre is that they will sometimes approach it with the attitude that they are writing something that nobody has ever thought of before. It is a new, different, groundbreaking approach, with new, different, groundbreaking ideas that nobody else has done and nothing can compare to--
And that simply is not usually the case. Finding comps can be hard, it's one of the worst parts about querying, etc., etc., but in many genres, you are not inventing something totally new. You are not the first person to think, what if this romance novel doesn't need to have a happy ending (spoiler alert: it's not a romance novel). You are not the first person to write queer polyamorous urban fantasy. You are not the first person to write a book with queer characters or disabled characters or non-white characters or non-Christian characters. Your groundbreaking new idea for a sci fi thing that you repurposed from a fanfic, that just feels dated and derivative, because it is, and anyone who knows the genre would know that.
That arrogance and that dismissal of existing publishing history and norms shows in people's writing.
Anyway, read books. They're actually pretty great.