Menu bar - http://en.wikipedia.org/wiki/Menu_bar#Ease_of_use
iPod click wheel - http://www.ilounge.com/index.php/news/comments/apple-receive...
I have no doubt that they would protect these if other companies infringed upon them. They offer significant usability advantages that Apple doesn't want others to have.
What we're seeing now is a bit different. The market is moving so quickly now that Apple is trying to setup some boundaries that they don't want others to touch. I don't think they really had to do this with these examples. I'm not saying any of this is right, I'm just not all that surprised by it happening.