Now, I will be careful as to avoid any "political" discussion about the two OS's here, but in my mind there are two main reasons for this.

The first reason is the fact that most home PC users (and thus a large proportion of the globe's computers) run some version of Windows - therefore, for maximum impact and publicity, people attack this OS.

The second reason centres around security - for one thing, most Windows users and Sys Admins charge around as "Administrator" all day long - if they contract a virus, this can wreak havoc as the administrative user that executed it. In the *nix world, any knowledgable user (and any Sysadmin worth their salt) will operate as a normal limited user, only suing to root as and when required - so any malicious code executed will have a very limited effect on the system - if permissions and security are tight, the worst that will happen is any files in your home directory will be destroyed. Obviously, UNIX security must be implemented and maintained to be effective, so much so that whole books have been written about it.

Cheers
ZB