I just started playing with calibre, and like it a lot (in fact that's why I'm here). I understand the metadata vs. directory structure issues and the advantages of metadata. Unfortunately for some of us, such as me, its not just a question of preference or being unreasonable. In my case there are "legacy" issues--my directory structure is integrated into pre-existing arrangements.
1) Most of my stuff is work and research related. Those books are in directories that I sync between my laptop, desktop, and work computer using a commercial server. So everything going into one "black box" folder means everything gets synced, including personal books. There's a dollar cost there, probably not much, but still

. Plus I have "SF" novels stashing on my work computer, which doesn't look good. If there's a workaround, that would be great (maintaining two lots of book directories isn't an option for me--space is at a premium).
2) The other problem is I use a reference manager (zotero) with all the citation info, tags, notes, and URLs to the relevant books. Messing with the directory breaks those links. It's a considerable number. Redoing these to the calibre directory structure is not a dealbreaker, I think, but certainly an inconvenience.
This isn't a criticism of calibre, but simply pointing out that for some of us our attachment to our directory structures has more to it than simply not "seeing the light".