I'll be honest, this article came as a surprise to me.   Not that Linux was making inroads against Microsoft, but that anyone actually used Microsoft to run a server.   I never have.  I never would.  It seems absolutely maddening to even try.

The NY Times has the scoop and says there is a cost issue:
Linux may actually be more expensive than Windows, as Savio Rodrigues highlights when comparing Red Hat Enterprise Linux pricing to Windows Server pricing on Amazon’s EC2. Not surprisingly, Microsoft has its own pitch on why enterprises should choose Windows over Linux, arguing that cost considerations favor Windows, not Linux.
But it is secondary to me, and indeed to the nearly 80% of IT people who say they will be adding more Linux instead of other OS flavors.   It's reliability:
67.5 percent of survey respondents cite “technical superiority” as the reason they choose Linux. Microsoft may still have the edge in terms of lowering the bar to development and deployment through development tools and the like, but Linux appears to have replaced Unix as the operating system enterprises trust with their mission-critical workloads.
The NY Times urges some caution on those statistics because they came from the Linux Foundation and their methodology was suspect - of 1,948 respondents, the Linux Foundation only reported on the largest 387.    So the percentages may be different but I doubt the overall meaning is less clear.