Not a fan for a few reasons. Flathub (as far as I know) works on the app store model where developers offer their own builds to users, which is probably appealing to people coming from the Windows world who view distros as unnecessary middlemen, but in the GNU/Linux world the distro serves an important role as a sort of union of users; they make sure the software works in the distro environment, resolve breakages, and remove any anti-features placed in there by the upstream developers.
The sandboxing is annoying too, but understandable.
Despite this I will resort to a flatpak if I’m too lazy to figure out how to package something myself.
This is theoretically an issue however in practice Anubis only weighs requests that appear to come from a browser: https://anubis.techaro.lol/docs/design/how-anubis-works
I just tested my instance with Jerboa and it seems to work just fine.