I have read the "Beneath the Metadata: Some Philosophical Problems with Folksonomy in the November 2006 DLib. Boy, did I have problems with it, but so did David Weinberger, who responded with Beneath the Metadata - a reply.
My reading of the DLib article brought back the pain of taxonomies and the "expert" arrogance that occasionally accompanies taxonomies. I have worked in many enterprise organizations who have gone down the taxonomy route and had decent results. Taxonomies are essential parts of building information management tools. But taxonomies are never done, they are not easily emergent, they are incredibly resource intensive (they need a lot of money and people to build them and maintain them), and they don't work for everybody (sometimes large portions of the people who use the information system can not find or refind information they want or need using the taxonomy). When we would survey the people using our intranet or the internet application, one of the top responses was things were difficult to find as they were not called what they expected them to be called. This can be before or after a few hundred thousand dollars were spent building a taxonomy.
This assumption that the author of the "Beneath the Metadata" makes that taxonomies are great and help people find things by providing the authoritative terms is wrong. Taxonomies are always less than perfect and most often far less than perfect for helping people find and refind information they need. But, we do need taxonomies to provide that foundation structure. We need solutions that can help the many people whose terms and vocabulary are left out of the taxonomy.
What should fill the gap for the failures of taxonomy? Yes, folksonomy should provide the emergent terms. The folksonomy identifies the many gaps in a taxonomy. The folksonomy provides the terms that can fill the gaps. The taxonomist/ontologist has the job of sorting out how to add the terms to their corpus (hierarchy, thesaurus, etc.). The folksonomy can even sit side-by-side with a taxonomy as the folksonomy is built from real people placing terms that they call things and their context on items they want to hold on to. It is their hooks for finding and refinding information. Tags should never be removed as that breaks a person's ability to find and refind that object. At the core of what a taxonomist does is aid the finding and refinding of information, thus removing a tag is breaking people's ability to do that, which means the taxonomist is flat out failing at their job.
The taxonomy and folksonomy are co-dependent. The two tools need each other. The both have strong proven advantages and they both have their faults. But the brilliant thing is they each strength provides cover for the other's detractors. The sooner the "experts" understand this the better off real people will be in finding information they want and need, as well as refinding that information.