Microsoft runs all Microsoft servers afaik. They used to use IBM AIX (Unix) servers for the finance department, but they contracted this work out to a third party in order to use entirely Microsoft servers.
So you're saying that a secure OS is defined by how many people are using it? So, DOS is more secure than Linux? I don't agree with that train of thought.
Whether you agree or not its true . A smaller user-base means two things:
1. That it is harder for a virus to spread around; as the means of a virus or spyware/malware being transmitted are usually from one computer to another, or a server to a computer. And if your using Linux, and %99 of the world isn't, then %99 of the people/servers you engage in some kind of connection with cannot exploit your computer with security flaws or viruses because they have a different OS. Intrinsically meaning the virus or whatever is not designed for the OS that you have.
2. Less people are trying to exploit an OS with a smaller user-base since it won't be as effective. The two main goals of exploiting an OS or creating spyware/malware or a virus is Notoriety or some Financial reason. Neither of which make it feasible to exploit smaller user-base Operating Systems.
Whether or not you agree doesn't change the fact that its true. I say I have a six-pack abs, but that doesn't make it true ;-P