They're trying to keep Google in its place, and prevent HTC from extending it. They're happy with Android being out there for the dorkwads and ideologues (it lets them shed their 'worst customers') but they don't want the public to see a sea of direct clones of their style of multitouch.
As for your point, that you feel patents like the multi-touch patent are justified, I would point out that many people disagree with trivial patents such as this, or even software patents in general. It is developers and IT people that are upset with Apples highly controlled development environment. Alienating this group of people may eventually backfire.
I don't feel that the patents are justified -- I'm merely explaining how and why I think Apple is using them.