I've been using Dokku [1] for a few years on a small setup, surprisingly without a single problem, taking into account it was written in "not-so-cool" bash. And I was considering Flynn as the next step if I need to scale it because Dokku doesn't have clustering support (added: looks like clustering support for Dokku is in work [4]).
After many checks, I got the impression Flynn simply wasn't there yet. Either because of low development pace, low number of supported appliances, or something else, I'm not sure. In the end, I picked up Ansible for more distributed installations.
[4] https://www.reddit.com/r/devops/comments/bgpw5w/flynn_vs_dok...