I had the same problem with my laptop.
First, try a:
$ glxinfo |grep 'direct'
to see if the direct rendering is really disabled. You should have an output like this:
"direct rendering: No
OpenGL renderer string: Mesa GLX Indirect"
If the answer is 'No'
, then the problem is that when you install fglrx, the library /usr/lib/libGL.so.1.2 gets overwritten from the proprietary version from ATI.
This library does not work with the radeon driver, so even if you reconfigure X with radeon, direct rendering will not work. You need to ovewrite again the library with the one from Xorg.
Of course, the package which contains this library depends on the distribution you are using, if you find this out you can reinstall the package and have the original libGL.so library in place.
You can eventually copy the library from some other installation in another PC.