If for whatever reason your .htaccess settings got messed up, the best option might be to just delete them from your server while you figure out the issue. To do this, go to Tools > Remove Website Access Manager From Server. A window will appear showing you which folders contain uploaded .htaccess files. If you choose to remove all these files, your .htpasswd file will be removed from your site root as well. Click Next to remove these settings.
If all else fails, use an FTP client such as Direct FTP or Free FTP and either delete the .htaccess file from each folder, or edit the existing .htaccess file and remove all the text between these lines:
#### CC BEGIN WEBSITE ACCESS MANAGER ####
#### CC END WEBSITE ACCESS MANAGER ####
If your FTP program does not show any .htaccess files, you may have to enable the option to show invisible files.