This is how I made it work.
Make a debian 11 qube that provides network with autostart and has the network-manager service.
In the template, install the protonvpn client
You should now be able to test the vpn works by using the gui client.
If everything is working, you can make a logon script that uses the cli client to automatically connect the vpn at boot time.
Assign the vpn as netvm for the qubes you want to use the vpn.