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The file systems are completely different for a start. If a virus gets into a linux partition it will only damage a particular file, which can be repaired easily. Windows shares everything across it's many programs and a virus will spread like wildfire. Linux is popular and becoming more and more popular as people realise the true cost of running a windows box.
I'm just gonna direct you to this article, although a few years old, still relevant. Of particular note is#5 on their list: http://www.pcworld.com/article/202452/why_linux_is_more_secure_than_windows.html