the reason the .htaccess is not in the zip file is that WordPress' svn does not allow it to be in the zip file... For the message:
###Threads###
See: http://wordpress.org/support/topic/db-backup-folder-visible-to-the-public?replies=36#post-1157221 for the thread, for me, back then it was the wrong path. (see also http://forums.lesterchan.net/index.php?topic=3714.0)
###for Dreamhost:###
How To Fix WP-DBManager WordPress Plug-in Error Message Fortunately, the fix is pretty easy. Go into the DB Options under Database in your WordPress control panel and change the Path to Backup to NOT include the .directory whatever it is. In the example above, delete the /.swami/ part of the path. That leaves /home/domain.com/wp-content/backup-db. Save the changes and then click on a different plug-in or control panel option and then back on the Database (to get it to re-try and read the file). The error message should disappear, and more importantly, your backups should be working again. You can test if WP-DBManager backups are working by clicking Backup DB which runs a manual backup. (http://besthubris.com/computers-internet/fix-wp-dbmanager-error-warning-your-backup-folder-might-be-visible-to-the-public/)