A minority, to be sure. But ultimately I am worried about the ability possessed by myself, my team, and potential hires. Not that of the average Linux user not working on the problems I am working on.
The argument for how the ability to do this is beneficial is not predicated on general users being able to do it, but the people administrating the services in question being able to do it.
If you have the ability to do so, it's possible in Linux (or the other open source OS). It's simply not possible in Windows.
Whether or not that's a huge deal is up for debate, but you're not really attacking a part of the argument that's relevant to their original point.
We're talking about a product designed to be run on multiple servers, in a datacenter. At that level, you're generally talking about professionals.
(edit: clarification)
When I run into a problem on my Linux machine, I typically have to do a lot of searching. More searching than I must do with Windows, because while there is generally only one Windows (at least relative to Linux), there are hundreds of Linuxes, distros and versions of those distros - many that are majorly different than the previous version.
Do you think it's easier for the average Linux user to find answers?