A post by John Carmack called Re:I've re-installed my Windows partition on Slashdot re-affirms id's intent to continue to support Linux with the release of their upcoming Doom game, though it will likely only be NVIDIA OpenGL support out of the box in the still far-off first test release:

We are still supporting linux.

The only downside of the next product is that initially it will probably only work at full feature level with the Nvidia OpenGL driver, but after the first test gets out (still a very long time in the future), I will jump back in to the driver development to try and bring the other open source drivers up to par.

John Carmack