Have you followed the directions on nvidia's webpage to install the nvidia video drivers? Your distro isnt going to support accelerated 3d out of the box.
of course without these drivers, i woudl be suprised to see it run at all. There may be some fruit in the effort to dig in the archives and try a few different versions of the driver, they have released broken ones before :P
http://www.nvidia.com/object/linux_d..._1.0-7664.html
That being said, dooms 3 is a rough game to run even on a properly congured windows box (its target platform, right) Which geforce card do you have? the hardware might just be a bit too slow for the game..... I woudnt expect my ti4200 to run it well under windows or linux.
Are you using cedga?