I fully agree with using Qubes, but I also think for most people in most cases that's akin to putting a bank vault door on the front of your house. I guess the question I would ask is: gun to your head you have a choice between running a random Setup.exe in Windows, a .sh/.deb/.rpm in linux, or a Flatpak. Which one are you choosing? 10/10 times I'm choosing the Flatpak myself. It might not be perfect, but it does seem better than most alternatives everyone uses all day every day.