Of course when you have ONE GUY doing the ports in an untimely fashion and not really officially supporting the client (Doom 3 wasn't advertized ANYWHERE, it was on an FTP server that was CONSTANTLY over capacity, etc), you're not going to get a great response from the community. They spent zero efforts advertising it and zero time appealing to gamers on Linux, are they really surprised?
Thanks for the Doom 3 source though, that is something I hope they continue doing... it drives forward open source game development.
Edit: Not to mention, they have no reliable metrics for how many people use the Linux version anyway! I remember buying the Windows version once the Linux client hit, and I just don't see them knowing I'm a Linux customer and NOT a Windows customer.