Kubernetes for the basics is actually pretty easy despite what people say, I got a fairly simple cluster running with little pain but...it doesn't take long before you want multiple clusters, or vlan peering, or customising the DNS or.... and that is when it becomes complex.
What will fly.io do? Probably what everyone else does, starts simple, becomes popular and then caves in to the deluge of feature requests until they end up with an Azure/AWS/GCP clone. If it stays simple, lots of people will say that you will outgrow it quickly and need something else, if you increase functionality, you lose your USP of making infrastructure easy.
I think perhaps the abstractions are the problem, if you are abstracting at the same level as everyone else e.g. docker images, orchestration etc. then I don't understand how it can ever work differently.
To make my point, the very first comment below (above?) is about container format, a really fundamental thing that noobs are not likely to know about, they will just immediately have some kind of error.