Thought I'd post how I solved the problem.
First, I probably didn't describe my situation well. I had installed the
Java EE flavor of Ganymede, so I didn't need to install WTP 3.0.1, but rather update it.
I posted on the Eclipse site, and someone mentioned that before trying to update packages, you probably first have to enable the webtools update site. It is disabled by default (they all should be, except the basics) and it can be enabled on the manage update sites dialog.
I did that, and it solved my problem - I was able to update to 3.0.1.
Hope it helps