I haven't actually had to install quake from a windows version cd since I purchased the linux version, but from what I have read you should be able to install by doing the following..
As root install the 1.32 pointrelease. Once that is done, copy over the pak0.pk3 file to the /usr/local/games/quake3/baseq3 directory.
That should be all that you need to do. I found the instructions here
Maybe the problem has something to do with a combo of the quake demo and the retail pointrelease. By the way, make sure you grab the 1.32B version
of the pointrelease for linux. I run Q3A on RH9 also and had a problem with my mouse not working (buttons worked but thats it). It has something to do with the new version of X I believe. Hope this helps you out.