This article doesn't talk about actual VMs/instances running in Azure. Also, so many new service devs only target Linux, and Windows is an after thought. No wonder 60% of the market place is linux.
the actual talk (video in article) says more than 60% of VM vcpus are from linux VMs, it does not talk about instances though. But I would expect Linux to be a lot of very small and very large VMs :)