That's an important note, indeed. Flux is a pattern as well as a library that represents an implementation of the pattern. Redux is another implementation (and a better one at that, in my opinion.) Specifically regarding Greyrest's concerns about many changes across many files - this can be reduced substantially using Redux.

With all that said, I still wouldn't consider FluxJS a bad place to start, as it provides a very clear example of what Flux really is, but once you understand how the pattern works you'll understand where the implementation is lacking and how Redux can help with that.