Comment by johnklos
There are many, many things that can't be hosted in Docker. For instance, literally everything that I run on many of my servers can't, because Docker only supports certain platforms and architectures. Things that we want to run on systems with modest amounts of CPU and memory can't be run via Docker for obvious reasons. Stuff that needs hardware access can't. Stuff that needs finer resolution of permissions can, but there's a lot more work that needs to be done.
But even ignoring those, if I'm going to spend all the time needed to containerize everything in to Docker images myself, why wouldn't I just run the programs directly and not deal with the overhead and extra work?