"What a new Internet might look like is still widely debated, but one alternative would, in effect, create a “gated community” where users would give up their anonymity and certain freedoms in return for safety. Today that is already the case for many corporate and government Internet users. As a new and more secure network becomes widely adopted, the current Internet might end up as the bad neighborhood of cyberspace. You would enter at your own risk and keep an eye over your shoulder while you were there."
Lack of anonymity is not the solution in my opinion, and even if it was, it would be almost impossible to prove someone's identity, which John touches upon in his last paragraph. Instead it is the lack of education on how to properly and safely use your computer that is the main issue. Even if a new Internet was created where users had to give up their anonymity, it would still not stop users who got infected via other means from infecting other users of this secure network. Yes, certain sites may not exist that peddle malware, but what is to stop a legitimate site from getting hacked and distributing malware?
So how do we protect our computers from malware? Education and the proper security software and hardware. Once you know how to safely use and protect your computer, you have gone a long way to making sure you do not become infected. The article, though, is a very interesting read and I suggest it for anyone interested in computer and Internet security.