As a Fedora user you actually have 3 choices in many cases:
- Fedora’s official repositories (traditional / rpm packages)
- Flatpaks From Flathub
- Flatpaks From Fedora’s official flatpak repository
I don’t have a simple and definitive answer for you but here are two things you should understand about flatpak and flathub.
- Flathub is a repo that has some verified and vetted software, it also has a lot of unofficial software that is submitted and maintained by individuals form the community who are not affiliated with the developer or with flathub. In the case of unofficial software, you should be cautious and vet it yourself to the extent you can, or choose a different option.
- Flatpaks are intended to be andboxed. But sandboxing depends on the packager/publisher of the individual flatpak so you shouldn’t count on all (or even most) flatpaks being properly sandboxed at this point in time.
Personally, I don’t have a super defined strategy. Typically if its (1) proprietary or (2) something I’m just testing out and will probably uninstall, I opt for flatpaks. If its something that needs or would benefit from deep integration with the OS I tend to opt for traditional packages. Beyond that I don’t really have a super strong preference one way or the other.