"it asked me for my root password after the download"
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*Which* download do you mean?

The klik client download+install
Code:
wget klik.atekon.de/client/install -O -|sh
may indeed ask for the root password, on that one occasion, to be able to add the 7 mountpoints to your /etc/fstab. After that, no more a klik-induced root password is asked! However, if the application run via klik would ask for the root password in "normal" installation mode too, this also happens with klik, and is quite normal. I am not familiar with Kid3 to comment more.

This is documented in various recent publications about klik. I suggest you to look at these resources, before talking in public about klik:

--> http://klik.atekon.de/wiki/index.php/User's_FAQ
--> http://dot.kde.org/1126867980/
--> http://www.kdedevelopers.org/blog/418