I would respectfully disagree with these replies =). The answer to the question is "Yes, you can use one configuration / processing server (virtual or physical) to protect both virtual and physical machines". The documentation is slightly 'fuzzy' on this topic, and unwittingly implies you need a physical configuration server for the physical machines, which is not true (it doesn't really make sense when you think about it, why would you?). And 'workload' does not imply virtual vs. physical - it's more about 'workloads with similar characteristics' such as file/print vs. SQL vs. Application etc.
Yes, if you had many machines, say 50 were SQL with large databases and high churn rates, and 500 were general purpose app/file/print (and both of those workload types consumed the same amount of storage for example), you may have multiple processing servers, one or more for each workload type depending on the numbers - but it doesn't matter whether the configuration servers (or the servers being protected) are physical or virtual. And it is also very related to your environment. If you had 1 x physical SQL with a small database, 1 virtual machine with a large database, and 8 VMs for File/Print and light applications - would you expect to install more than one configuration / processing server to replicate them to Azure?
Consider a private cloud IaaS scenario where you are unable to access the underlying VMware hypervisor since it is shared with many customers - in this case you have to treat the VMs as 'physical' machines and install the mobility agent, just like you would on a physical server.