The struggle between malware and the PC dwarfs the struggle between Free and non-free software. Various estimates based on recent studies put the percentage of infected machines in the 31-50% range depending on whom you ask and this is in spite of widely used anti-malware software. The defence is totally inadequate.
On the other hand, using FLOSS is an excellent defence against malware since almost all malware is aimed at that other OS. Even if that were not the case the relative simplicity, openness and modularity of GNU/Linux gives fewer vulnerabilities and better systems for fixing them.