Flynn itself costs $3,000/year at the most basic service level, before you even start covering infrastructure. Why shouldn't I just write what I need in a few hundred dollars worth of hours?
Flynn co-founder here. Flynn is free open source software and always will be.
Our managed service is for users who want to outsource the management of the cluster to us. There's no secret extra technology (it's just Flynn underneath), what you pay for is a professional ops team to manage your cluster. The service is also freemium (and free for the vast majority of users).