In my mind Flynn has more of an application focus - something comparable to Heroku with git deploys etc.
I wanted to run a regular (every 10mins) task. I created a container that had the hyper cli installed that spawned a task container that exited on completion. This worked really well for what I was doing. They're thinking of adding this as a hyper sh feature: https://trello.com/c/JfyGyBKS/45-serverless-cron
I didn't consider using Flynn. Just didn't really have Flynn down as being for this kind of thing. Of course another difference is that Hyper.sh is a service; Flynn is a project that I need to self host.