I found both easy to get started with. Flynn works well with DO and AWS although I couldn't get it to work with any third-party hosts (ssh auth issues).
Took me about an hour to setup 3 load balanced nodes and deploy their test go app which writes to Postgres.
There are issues with Flynn though:
- Missing Dokku's rich plugin support (Let's Encrypt is a breeze on Dokku)
- Log shipping
- Docs need work. I had to dive into the issues to figure out how to setup the custom domain names
- The HA is a bit murky. I downed two of my three nodes and the cluster collapsed. Since Flynn runs on one machine I expected it to work
I personally think there is a big gap in the market for a company that can provides a thin layer on top of the various IaaS providers to create the ease of Heroku with lower costs.