No, no, you're right. iTunes does have some usability issues still. The "removing a song from playlist" is actually the first one I'd think of also; the fact that you hit the same button to delete a song and to remove it is problematic. By default iTunes pops up a warning either way asking you if you're sure you want to delete/remove, so that that way you know what you're doing, but if you tell it to stop popping up warnings there's a risk of messing things up.

The thing is that anything can become intuitive. Use Amarok long enough and I'm sure it becomes effortless. The term interface design uses to describe this is "mental model"; good designs let users form a model of how something works before they even touch it. (So on iTunes, the metaphor of seeing album covers immediately makes me think that to play an album I click on its cover, which is exactly right.) It's very difficult to create a program that forms a good mental model of every single function at once, especially if you're making a complex program like iTunes. But I'd argue that it's still vastly easier to intuit from the interface than it would be for Amarok, where, looking at that screenshot, I can't tell how I would look at other artists' music or how to form a playlist or a number of other relatively trivial tasks.