Note: This pertains to version 0.1 of the plugin. Not showing hidden folders will be incorporated in later versions.
First, with the hidden files, you should be able to easily block them from showing by adding the extensions to the Forbidden File types list. So, to not show hidden file such as "desktop.ini" and ".@__thumb", just add: ini and @__thumb to the existing list of htm;html;php (of course, separate via semicolon). So it would look like: htm;html;php;ini;@__thumb.
Second, with hidden folders, such as .svn, CVS, .AppleDB, .AppleDesktop, you will need to edit the plg_easyfolderlistingpro.php file. This is located in plugins->content. Replace line 653 with:
Doing that should fix your problem. Of course, if you are not comfortable editing the code, you could either wait for my next software release, or just delete the hidden files and folders. So, you have various options.