If your using debian/ubuntu, the reason for this is most likely due to the fact that inside /etc/apache2/sites-enabled/000-default /var/www is set as follows:
Options Indexes FollowSymLinks MultiViews
allow from all
Which will override your changes defined in httpd.conf.
In order to allow processing of htaccess Options for files inside /var/www, you will need to change the AllowOverride line from that file to something other than None.