Flatpak repositories cannot be disabled
Fedora 35, gnome-software-41.3-1.fc35.x86_64.
I am not able to disable Flathub or other Flatpak remote from GNOME Software:
I am not sure whether this is a bug or a feature since there are some apps installed from the remote. However, it is possible to disable rpm repositories (except some which I believe are marked as system ones) even if there are apps installed from them.