Flatpak seems to follow a similar path as many other Linux technologies like Wayland or Systemd, in the sense that they seem to arouse the anger of a small but very vocal crowd who really can't stand any challenge to the status quo. So this is the template of the story: There is a new tool or workflow trying to replace or complement an old one. This new tool tries to solve many different complex problems that the old…
Why do you assume that such people don't understand this? Sometimes those compromises mean that the tool can no longer accomplish something important to some users.
I don't think that being upset that software has become less useful is terribly unreasonable or hard to understand.
> Additionally, as it's natural with any new technology, the very first incarnations of the new technology are not very mature and there is a lot to polish, a lot of tooling missing
And while the software is in that state, it shouldn't be forced on anyone. It's not unreasonable for people to want to use software that actually works well in the present.