I think Flux architecture is more than just a Pub/Sub messaging system. It's true that Flux Stores broadcast (publish) changes so that subscribers (views) can react to these changes and update themselves. But if you have developed using Flux, you would know that Flux is more of an architectural pattern rather than pub/sub system.
There are a few rules and assumptions in a Flux based app. For example, all the data should flow into the Stores through Actions. Similarly, the data flows out of the Stores via listeners. It promotes unidirectional data flow and you have a clear idea about how the data flows throughout your app.
See the following articles to have a better idea about what problem Flux solves :