Maybe I want to find all the functions related to assignment: how do I do that? Do I just look on disk? Do I use tags or metadata? Do I assume some naming convention? It's a problem you have to solve somehow, and solving it requires effort, because it's an explicit organizational effort. Modules or namespaces or packages or classes give you a way to say "this stuff goes together" and to encapsulate and abstract large units of related functionality, and to do so in a way that tools and programs understand. In a Java IDE, my IDE will auto-complete all the functions on a class; in a REPL I can just print out all the methods on an object. That's a useful organizing principle, and it's one that you lose if you totally flatten the namespace.
You could argue that organization isn't one-dimensional or hierarchical, which is what namespaces and such force on you, and it's a reasonable statement. But replacing it with nothing explicit and relying on extensive developer metadata and documentation so you can search for things? That seems even more idealistic. When was the last time you saw every single function, even private ones, documented and tagged so correctly and up-to-date on a real-world, large-scale project that you'd rely on them to serve as the only organizing principle in your application?