If you would rather use an updated calibre 2.x, it is still possible to enable the system tray:
Run from source and revert this commit:
https://github.com/kovidgoyal/calibr...3f08edfcf40348
It will re-enable the option on linux, which will work for some desktop configurations and on other configurations will irretrievably hide calibre requiring "killall calibre" to get it back after minimizing.
On my system it works. (Arch Linux, cinnamon-desktop)