This has always been a major difference between Mac OS and Windows, and I personally prefer the way it's handled on Macs. I like being able to close all windows associated with an application but not quitting the applciation. Far too often I've closed my last Mozilla window (not realizing it was the last) at work and had to wait for the entire appliation to relaunch so I can keep tabs on my mail.
I also find the fact that Windows puts every window, minimized or otherwise, in the taskbar rather annoying. Having more than a few windows open makes it appear really cluttered and I find it impossible to find anything in it quickly.
To the point about the little black arrow being overlooked I would have to say that if you're looking for open applications then you're looking for the black arrow, and it isn't that hard to see. I like the Mac OS 9 application list better, and I think the dock has a lot of problems, but I don't think this is one of them.
If it has syntax, it isn't user friendly.