This is something that Windows administrators hear a lot, especially from *nix or storage folks. There's a stigma surrounding Windows and it is reflected in both compensation and respect in a lot of organizations. Open up Dice or Indeed and see how many six-figure Windows jobs you can find - now do the same for storage or Linux administration. There are certainly top-tier Windows gigs available, but they are much fewer in number than the others. I think that this disparity is caused by a few different factors:
You can do a lot through the Windows GUI
The most common knock on Windows is that everything is point-and-click. This is, of course, not true, especially in the era of PowerShell, but the myth persists. In many cases the GUI in Linux is limited and most Linux servers are installed without a GUI anyway. This forces Linux administrators to be intimately familiar with their command-line interface, which eases them into scripting. Linux admins have been laughing at us for years in this department - they had bash, dash, zsh, tcsh and we had cmd.exe. They had every right to gloat about this....until PowerShell was released.
Everyone knows Windows
Growing up in the 80s and 90s, almost everyone is heavily exposed to Windows on the desktop, whether it's in school, at home, for gaming, etc. Many IT professionals considered themselves as "power users" before they got into IT. Unfortunately, the ability to overclock a GPU or install StarDock doesn't translate into useful skills for an IT pro.
Microsoft didn't play the cross-platform game until recently
This absolutely isn't the case today. With many components of the .NET stack being open sourced, Linux on Azure and Hyper-V being a first class citizen, and much of System Center and other management tools supporting OS X, Linux, and Unix IT pros have a much larger set of options than they did in the past. If you go back 5 or more years, the cross platform story was not a compelling one, so many organizations that didn't want to be locked into a platform looked at OSS over Windows. This lead to a number of Linux/Unix folks feeling that Windows simply wasn't suitable to run their business on.
The reality couldn't be farther from the points above. When you're talking hybrid cloud with System Center, Hyper-V, Azure, and PowerShell, there's an amazing end-to-end platform that simply doesn't exist elsewhere. For the tiny two person dev startups, this might not be a compelling idea, but for the enterprise that's struggling to understand how and where cloud fits for them, it's critical. When you're looking at ExpressRoute, Azure Pack/Azure Stack, PowerShell DSC, and System Center there's a lot to like.
So, if you're a Windows admin, don't take any crap from the Linux guys at work. Microsoft loves Linux! Skill up on Azure, learn automation, and venture into the brave new cloud world that we are living in.