Some of the highlights:
* Fair use is a limitation on rights pertaining to intellectual property, while net neutrality is a limitation on rights pertaining to physical property--Lessig's own excellent book Free Culture points out that intellectual or creative property is different from physical property in significant ways.
* The burden of proof on a fair use claim is on the person claiming fair use, not the copyright owner; in net neutrality the burden is on the property owner.
* Fair use is really a limitation on a government regulation (copyright), while net neutrality is a regulation that's a limit on business models, contracts, and technology.
* Net neutrality advocates have not been clear about what they would require and prohibit, how violations will be detected/measured, and what the enforcement mechanisms will be. (I don't trust Congress to tell network engineers how to do their jobs.)