I presume the .htaccess that exists is what the panel created for you, which shouldn't contain
however it's also possible that "-Indexes" is being inherited from a directory above (and that .htaccess might have been installed for you by a CMS such as wordpress).
If that's the case, you probably want to leave the "-Indexes" in force for the directory above and instead edit the .htaccess that was created to add the user/pass and add a new line to the file:
Which will reverse the "Options -Indexes" that is being inherited from above.
This is just a guess, I don't have any idea the structure of your domain, but normally by default you should see the auto generated Apache index.