Hi, sorry for late reply. Of course you can display any files from your upload folder if you paste in the direct link. (Otherwise your website wouldn't load up as all content would be blocked by the plugin)
This plugin prevent directory browsing, it doesn't prevent your files from loading. For example someone who don't have a full link to the .PDF file won't be able to browse your server or the /Upload folder to look for it.
I hope you understood my explanation about the concept of this plugin.
PS: If you don't want direct access to your PDF, install S2member for example, it requires a user registration to access specified files.