I'm coming into this thread late, but have had the same problem off and on over the past 12 months, and think I have solved it.
For people with domains, or even people without, server 2008 has a couple of different users/groups that represent the anonymous web user, and they're not always granted access by default to folders, even those in "wwwroot".
I'm not sure I've ID'd the correct circumstances under which folders do not inherit permissions properly, but I have noticed this: On a standalone 2008 server, when creating a new folder in Windows Explorer, and then making it the root of a web in IIS Manager, IIS adds the "IIS_IUSRS" AD security group to the folder with "read/execute" permissions.
The local IUSR account on the server, however, may not be a member of this group by default, and if this is the case, then the web will exhibit all the permissions errors described in this thread, and browsing the web will return a "401 unauthorized". I leave it the forum gurus to explain the relationship between "IIS_iUSRS" and the local "IUSR" account and under what circumstances this will occur.
Anyway, I found that granting explicit read/execute permissions to the local IUSR account (by adding it under the folder's security tab in folder properties), will fix the problem, as intuitively it should. I presume that adding it to the "IIS_USRS" group in Active Directory would have the same effect, since that group is granted permissions on the folder when it's made the root of a web in IIS Manager.
That's my empiric experience...hopefully someone can explain what is the "root" issue of the problem.