There is no Intel Indeo Video Codec for Mac OS X. Most likely the instructions refer to OS 9 (and its System folder).
The System folder in OS X is supposed to be not modifyable, so your permissions are set up correctly.
If there were an Indeo Video Codec for OS X, or if you want to install some other video codec for QuickTime, then it should go into the folder your-hard-disk/Library/QuickTime/