VirtualDocumentRoot и всякие разные % (проценты) :)

<VirtualHost *:80>
  ServerName company.ru
  ServerAdmin webmaster@company.ru

  ## Vhost docroot
  VirtualDocumentRoot /var/www/vhosts/%0

  ## ITK statement
  <IfModule mpm_itk_module>
     AssignUserId vu_%1 www-data
  </IfModule>

  ## Directories, there should at least be a declaration for /var/www/vhosts

  <Directory /var/www/vhosts/%0/www>
    Options Indexes FollowSymLinks MultiViews
    AllowOverride None
    Order allow,deny
    Allow from all
  </Directory>

  ## Logging
  ErrorLog /var/log/apache2/company.ru_error.log
  LogLevel warn
  ServerSignature Off
  CustomLog /var/log/apache2/vhost_access.log "%V %h %l %u %t "%r" %s %b"
</VirtualHost>