How does a Dockerfile change things? Your application is packaged into a container. The Fly service runs any application not just web applications or build artifacts. Of course your application is going to get a complete operating system environment to run in.
I don't think the Dockerfile has anything to do with them pulling your container from their registry and running it on their server.
Ah right okay thanks. The point still stands the Dockerfile and image is used as a container for your application and does not imply a manage-it-yourself server is being used.