I have worked since 1996 on Windows servers (then NT 3.51) and Linux (then 2.0). I can assure you that Linux was much more stable than NT at that point. And more full featured - I didn't have to "go into the registry" and void my warranty to have more than a few IP addresses for my Linux machine (unlike my NT machine). I have found it the same since then. Besides from my own experience, I have know people managing Windows server groups at Fortune 100 companies who freely admit that Windows is a second-rate server compared to the UNIX servers (primarily Solaris and Linux), and that the main reason for the presence of Windows servers at the company was Windows monopoly on desktops.
Every UNIX specialist I know thinks Linux servers are more stable than Windows servers. Even most Windows server specialists I know admit Linux is more stable and full-featured, although a die-hard few disagree. In medium-sized to large companies, UNIX servers and UNIX-specializing sysadmins outnumber Windows servers and sysadmins.
Also aside from the difference between desktops and servers (the Linux core stress that they are focused on Linux being a good server, the desktop is less important to them), there is the old quantity becomes quality thing. Someone may have one experience with their own desktop, but when one begins dealing with thousands of machines running a certain OS, one becomes very familiar with its strengths and foibles.