Yeah, a lot of high-value secure systems run Linux and GNU. Web services, government systems, the vast majority (edit: it's now all) of the TOP500 supercomputers etc. I suspect at least part of it is that these systems get much more targeted attacks because of their high value, whereas viruses are to an extent un-targeted shotgun attacks. I suspect the economics of virus writing dictate that most of the effort is put towards the most popular platform, i.e. Windows.