Also if we imagine some person starting bookmark list from scratch, with tags - he has to A) make complete tag system from the beginning (I've tried, it's not easy) or he'll be forced to re-tag old ones later; B) type in tags (or select) every time he bookmarks site.With folder trees I use one click to drag&drop bookmark to the intended place.
Tags are the future but only if someone would be able to automate them completely.
On sets with 10-100 bookmarks type of index system is completely irrelevant - you can even keep them in a plain list and still don't waste time.