IMO, same reason they have their own repo, which eventually feeds into Red Hat enterprise, to have a trustworthy, curated set of safe (ish) software that's had eyeballs on it. A worthy enough goal, but that said, it applies a lot less to flatpaks. I personally used to remove theirs because I didn't like having multiple sources, now I'm on Bazzite which ships with flathub.

I asked this exact thing somewhere else, and the best answers I got were:

• there is a somewhat legitimate motivation for fedora to package their own flatpaks in the context of their atomic desktops project.
• they started doing this before flathub was established, and it was a better idea at that time.

So, as per usual with Linux, there are some obscure and historical reasons this is a thing, but it is useless for the majority of users. Fedora should really not have it configured as the default source for flatpaks out of the box

Wait, why is Fedora making their own flatpaks? I thought the entire point is that they work on any distro and everybody gets the original source from flathub.

Just to add to the other replies you've got, as far as I'm aware there's no reason why you can't add Fedora's flatpak repo on another distro. Why you would want to is another matter, but I think the fact that anyone can make their own repo is the fundamental strength of flatpak as opposed to snaps; it's not tied to one organisation, Flathub is the de facto central repo but it doesn't always have to be.