This is not always true. I can't speak for other universities, but ours does not pay a dime to Microsoft for licenses supplied by the MSDNAA program. We only incur the costs of hosting the CD/DVD images of the software they provide for students to download.
Microsoft has an incentive for providing their software to university students--specifically, their Visual Studio and Windows Server brands. They will license these out for nothing if it gets them educated, motivated developers, much like they often hand out Visual Studio disks at conventions and tech talks just for attending.