ProtonVPN actually has a flatpak, and it worked for me when I tested it out a couple months ago.
But my personal use case is with Private Internet Access. I basically had to install it from source, tweak the installer by commenting out some lines that tried to write to /usr (which is immutable), install and modify the systemd daemon service manually, then install the .desktop file for my local user. And for some reason, the OpenVPN tunnel doesn’t work, but WireGuard works fine.
I may try my hand at making a flatpak or RPM for a cleaner install, but it’s seriously made me reconsider if I want to keep this provider, move to one like AirVPN, or go with a different immutable distro like NixOS or openSUSE MicroOS.
If ProtonVPN has its package in the Fedora repos or as a downloadable RPM file, it should be as easy as rpm-ostree install protonvpn or rpm-ostree install /path/to/protonvpn.rpm.