We just published to Slide Share a new presentation on best practices on using Metadata instead of Folders in SharePoint 2013. You can find the presentation here.
In general, we still see lots of clients using folders instead of site columns in SharePoint because they are easier and more ad hoc. We also find that many of our clients don’t have a fundamental understanding of metadata and taxonomy concepts before setting up document libraries and therefore default back to a folder structure because it is familiar.
There are lots of good reasons to use SharePoint taxonomy features such as site columns, content types, term store, etc. and this presentation outlines some of those advantages.