The change was made in Transmission 1.30 by the Transmission authors;
their rationale is that the new default is compliant with Gnome
interface guidelines. (Which it is -- I'm not as sure about
convenience.)

See here:

http://forum.transmissionbt.com/viewtopic.php?f=9&t=6420&p=31112&hilit=tray#p31112

-- 
Transmission tray icon no longer enabled by default
https://bugs.launchpad.net/bugs/299661
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