you could always spend the money and purchase
accelerated-X (Currently the only option for you to have hardware acceleration with that GPU thanks to AMD/ATi's craptacular GNU/Linux support, this may change
IF AMD releases the source to the driver's as they have promised). Aside: there is a reason why long term GNU/Linux users will always advise you to
NOT buy an AMD/ATi video card and to purchase laptops that use nVidia GPU's.
Or start the game like so
./ioquake3.x86 +set r_allowSoftwareGL 1
to allow software 3D and enjoy the poor performance