Virus writers write for the popular operating systems. There aren't many viruses written for Linux servers in much the same way there aren't many viruses written for the Mac desktop. If the Linux community gets its way and becomes "the new Microsoft" of the server world, what will prevent the virus writers from just switching exploits and going after the numerous ones I see reported on Linux OS's?
There are several reasons why the prevalence of viruses is much more so on the Windows side than Linux/Unix. Technically speaking, Linux has a much better architecture with respect to structure and permissions. A virus received by a Linux user generally cannot infect system files because of permissions that are in place with Linux systems.
That same virus also doesn't affect programs or files belonging to other users on the box, so it is naturally better retained. Additionally, in order to attack Linux, the writer must be able to attach itself to executables, which run with system privileges. Only a token amount of Linux executables have root type privileges.
I would agree that if Linux did run the world, there certainly would be many more attacks on that operating system than there are today. There might even be a new breed of hackers and virus folk in place, much more intelligent and sophisticated than the current breed. Those who write viruses and worms want to impact as many people as possible, and certainly one of the main reasons there are more viruses on Windows than any other platform is because there are more people using PCs running Windows than any other platform. The bottom line is that these idiots want to hurt as many folks as possible, so they focus on Microsoft.
Though Linux is a better OS than Windows will ever be, as its popularity increases, I don't think anyone would disagree, so will its susceptibility to virus attacks. On the other hand, the Linux/open source community will probably do a better job in proactively fighting the virus fires than Microsoft can ever do.
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