From Google Online Security Blog:

"In this post we investigate the distribution of web server software to provide insight into how server software is correlated to servers hosting malware binaries or engaging in drive-by-downloads."

Their numbers are slightly different from Netcraft's ones, but they give a fairly good explanation about it. According to Google IIS and Apache are sharing the same percentage in the overall malware distributing web servers.

Interesting facts: in the US Malwares are served at 80% by Apache, in China at 95% by IIS...

From Google Online Security Blog