It all comes down to how the two operating systems were designed, as @sicarie was trying to explain.
With Windows, the reason it is so incredibly easy for people to write virus', is because there were now administrative separation of access to the registry. ALl users could edit the registry and it is like that today.
On Linux, there is a root account. Yes, root is god, but first you have to gain root access. Without it, you cannot access the files on the system that could do the most damage. The permissions structure on Linux/Unix is what makes it drastically different.
Even if you have a virus written on windows and yes, wine allows you to run it on linux, it won't get anywhere because the virus' (as sicarie said) cannot run on Linux, even with wine.
Besides, how many virus' do you know of for Linux? Its so incredibly entailed and difficult to write one that people don't bother. You get greater numbers of effected machines attacking windows and that's why they write virus' for it.