Software that is licensed per-server has a higher burden than just the license's purchase price: you have to actually keep track of those licenses so that you can plan and optimize license capacity (even if you have a site license) along with real things like server and network capacity. To me, as someone who works exclusively in open source environments, that is a heavy burden and I don't buy software that is licensed per-machine.
To get an idea of the difference in overhead costs I think it's helpful to look at Amazon's pricing between un-licensed Linux and licensed Windows instances. An m3.2xlarge instance with Linux is $0.532/hr whereas the same instance with Windows is $1.036/hr. That is a pretty big difference.
I'm not certain, but I'm guessing the difference boils down to two costs for Amazon:
1. The cost from Microsoft of a license of Windows
2. The cost of dealing with licensing Windows
3. The cost of support from Microsoft
52% cost overhead does seem a bit high, and I bet you could do better than that yourself, but I also don't think it is trivial. Just looking around to figure out the cost of licensing things for this comment was draining.