That's not an Apache or filesystem issue. That's a login failure to the dbms.
Double check the username and password for the root account for the (presumably) mysql login attempt. It is also possible (although IMO unlikely) that the root account is denied locally and granted remotely (just the logic of such makes absolutely no sense).
If you've forgotten your root password (try without one as well since the default is no password), follow the documentation here for resetting the root password (assuming you are using mysql): http://dev.mysql.com/doc/refman/5.0/...rmissions.html
BTW, I should mention: never use root as your user account. Use a user account created for JUST the database in question.