I work on both Windows server and Ubuntu server. First of all, both of them are secure and reliable. I ran a website with more than 15 million pageview per month on a single Windows server using IIS 7 and PHP via FastCGI. It is fast and stable. No downtime.
The problem with Windows server is that it is more expensive. It is not lightweight. You can roll a 512mb RAM 20GB Linux server for only $5. I don't think you can even run a Windows server with 512mb RAM.
Most great software for server are primarily built for Linux. Some will get port to Windows, but the support for those software for Windows sucks and buggy.
I think its a fairly broad question since there are some benefits to windows over linux from a development perspective. However I personally have used debian based linux distro's for the past few years I would say to anyone to choose the right tool for the right job.
However some of the benefits of linux may be :
Can be lightweight - Some linux distro's are extremely small so can be fully functional on older hardware
Customizable - Most required services are extremely flexible and can be removed and or modified very easily if source code is available
Package Management and software installation - Most fully fledged desktop distro's offer an out of the box package manager to keep software installation simple for new users and allow access to a huge amount of readily available software with one click, or using the terminal commands.
Open source - Usually, Most Distributions consist of packages that can be easily found and modified and so most aspects of the whole user experience can be changed