Apologies for necroposting, however as this is the first hit in google for this specific issue, I thought I'd throw in my two pence.
As was pointed out above, the installer adds three .desktop files:
Code:
/usr/share/applications/calibre-gui.desktop
/usr/share/applications/calibre-ebook-viewer.desktop
/usr/share/applications/calibre-lrfviewer.desktop
To remove this ridiculous behaviour in one move rather than working through every mimetype (including audio/video files??!!) by hand with xdg-mime (or whatever you choose), simply remove the MimeType=blah;blah;blah entries from these files. This will dis-associate the calibre components from
everything. You can then re-associate any single file types yourself if you so please.