They've taken several steps to amend that, and while apparently outright rewriting their licenses isn't good enough, they have recently made some small changes to loosen VM restrictions. They've removed the need to re-assign licenses if the virtual machine itself moves to different hardware, and removed the portion that limited companies to only being able to move physical hardware once every 90 days. A small change, but one that is probably encountered more often than many realize. One reason for the use of virtualization and virtual machines is to avoid becoming hardware-locked. Should one machine be insufficient, no big deal, just move your VMs to a more powerful one.
A lot of this probably has to do with Microsoft's increased focus on Hyper-V, a stock feature of Windows Server 2008. Now that Microsoft is intent on getting customers to use their virtualization suite, they need to make sure their licenses reflect that.