Fine Uploader only understands HTTP; not FTP. That being said, you could easily have Fine Uploader uploading files to an endpoint on your server, and then -- maybe after some server-side processing -- serve those files over (S)FTP -- or any other protocol -- if you would like.
Fine Uploader's primary goal is to normalize the file upload experience in all browsers. The pros of using this over an FTP client would be that any user that has a web browser should theoretically be able to upload files to your service. What your service does with those files afterwards (whether that be hosting them on an FTP server, transcoding multimedia files, etc) is completely up to you.
Hope this helps.