As for not closing apps, I find that hard to believe. Maybe if you only ever use 3 apps it is OK. Otherwise, why even have a mechanism for starting and stopping apps? Could just start them all upon booting. (Actually this will probably be the future, but not yet).
Also it is very confusing if you have closed all windows of an app, but not the app itself. Because then if you click the app icon, nothing happens (it is already started, after all).
If you close all the windows of an app, clicking the app icon in the Dock usually opens a new window. It does for Safari at least. Anyway, the main difference is that Windows doesn't consistently differentiate between windows and applications, and Mac does. On the Mac side, a window is just something that's opened up by an application as an interface, whereas on Windows, the window is the application, which is why if you need to open more than one browser window you have multiple instances of Microsoft Internet Explorer running, but it's really okay because secretly they're all running off the same DLL's. Or something like that.
By the way, the "unintuitive" things you mention aren't unintuitive, just different from Windows. It's no less "unintuitive" than whether or not you set your parking brake with a pedal or a hand lever (so better not get your mum a Toyota if she has a Ford).
By the way, OS X is good enough at multitasking and memory allocation you don't have to actually quit your applications. It's sufficient to just close the window. That way it starts up faster when you want to use it again.