i think its simple as this:

napster is not illegal. Only trading copyrighted material is illegal. The problem with napster is that it is a centralized operation with its own legal entity becuase it is a corporation.

Gnutella on the other hand is in loose terms a bunch of people trading files directly with each other. There is no way to shut down gnutella because it is not a corporation and nor does it have a legal entity. To shut it down you have to sue every single user, which is pretty much impossible.

Hope this helps.