Calibre is available for Linux so doesn't require Wine as far as I know.
You just download it using the firefox browser in Linux here
http://calibre-ebook.com/download
and then follow the instructions on this page:
http://calibre-ebook.com/download_linux.
But I understand your frustration. Linux just isn't that simple and the endless variations of it don't help with the learning curve. The Unity desktop that is used in Ubuntu now is also puzzling to me, mostly because I don't want to take the time to figure it out.