The article points out that it is too easy to create duplicate files. Part of that ties into what you're talking about. Part of that deals with how people deal with files (e.g. few people use versioning outside of software development). The article is suggesting that a strong hierarchical system will help to avoid that problem.

Of course the other problem with tags is management. Placing something into multiple relevant categories involves more effort. Failing to place something into a relevant category makes it harder to find since you are now dealing with either a flat file namespace (worse yet, a disorganized one) or a flat tag namespace. In theory, some of this can be handled by letting someone else handle the tags (e.g. the creator, the publisher, or the seller), but that has its own problems since there is frequently a conflict of interest (e.g. irrelevant tags are applied to increase the visibility of a product).

At the end of the day, we have to accept there is no perfect system of categorization. Some will prefer hierarchies. Some will prefer tags. From the tone of the article, it is clear that they prefer hierarchies.