So let me get this straight.. when an application has ONE WINDOW in OS X..
that is NOT the main application window? I mean.. there is only ONE window and EVERYTHING takes place within that window.. if thats not a "main application window", then what is it?
You're still confused. This is an OS X Window (Source: Arstechnica):
Note: it has a bar, at the top with no menu, and three colored buttons. When you click the red button it closes the window, because that is an action performed on the Window. It doesn't then Quit the application by default unless the developer over-rides that action (and he needs a good reason for that such as the application is so simple that no window is not useful - see the logic: window actions perform actions on the Window). It also has other qualities such as being movable, resizable and scollable, and it shows ONE concept.
The big thing that you keep on insisting is a Window has none of these qualities and is NOT a window. Here it is:
As you can see, it is not movable and doesn't have buttons and has none of the qualities that distinguish a
Window. What is has at the top is a menu bar. Within the menu bar you perform actions that affect the application (or the front window if there is one). See the logic:
Window buttons etc --> Window actions
This is the logic you seem incapable of grasping. Within this area, you can often view the windows of many applications only one of which will be in the foreground.
For example this user is 'in' Safari. But he can see other apps. This is not the Main Application Window. If you want to give it a name, either the 'screen' or the 'viewport' (if you want to be pedantic) would be fine. We don't usually need to refer to it though because we refer to the the Application menu as where we perform actions.
It certainly is not a window. People generally refer to it as the
screen .
Anyway, when an application has a single window and all activity takes place within that window, THAT IS A MAIN APPLICATION WINDOW. Even my friend's 3 year old daughter who just started using a computer could tell you that!
So this is why you're having problems. You are listening to your friend's 3 year old daughter. You keep on talking about a main application window. But most applications can have more than one window and that thing that surrounds them is not a window - it's the viewport/screen. See above.
Oh, and by the way.. when I press a button and the window scales down to the dock.. thats minimizing

Even Apple calls it as such
http://docs.info.apple.com/article.html?artnum=75459 "Command-M Window Menu
Minimize Window"
Very good. But you didn't say 'minimizing the window'. You said minimizing the application. Of course, a window action affects the window. But you keep trying to change this logic by saying the window action should quit the application.
Seriously, just admit you're wrong. You need to do that just as you need to quit calling people "beginners" who clearly have more experience in computing, and life in general, than you.
Clearly, you live in a parallel universe because pretty much all the comments on this thread have been explaining to you the logic behind the red WINDOW button not quitting the APPLICATION by default (and when when it does quit, it is for simple applications that have no use for zero windows). So what you are saying that all Mac users and all Apple engineers fail to see the truth that only you seem to see despite it working that way consistently for over 15 years (and working that way in Photoshop in Windows for example) and despite the many users who have on this thread given you the reasons for the way it works.
There's no need for me to quit calling you a beginner because in OS X that's what you are, and I'll happily admit that although I design, program, and build Japanese language websites and Kanji conversion systems, in Windows, I'm a beginner. Which is why I don't go to Windows sites telling them why I might think the logic of their system is wrong.
"Learn to quit properly" .. what a joke, seriously. Again, you're giving Apple fans a bad reputation, so please just quit already. I'm sure theres plenty of dedicated Apple fans who are reading this thread who are quite ashamed to be associated with a person acting like you are at this moment.
What planet are you on? Pretty much every Apple user on this thread has explained to you why and yet you insist on arguing something you don't understand, and supported my position. Plus the one user who PM'ed me thanking me for the explanations, and saying that he was used to quitting with alt-F4 on Windows and was worried about switching to Mac but this discussion and my explanations had made him decide to buy a MBP.
Misunderstandings. hah! Again, Apple never does any bad (just look at people defending the $20 ripoff upgrade for the iPod touch).
You talk about logic but you then throw in the straw man logical fallacy. I never said Apple does no bad. What does this have to do with anything in this discussion? Yes, it is a ripoff.
There was absolutely no "misunderstanding", just stating how applications should LOGICALLY work.
And finished with the circular logic fallacy.
You don't understand the logic, so to make it easy and to help you understand. The nice diplomat that I am here goes:
Application Menu > Quit :::: Quit the
Application.
Click
Window Button (default) :::: Close the
Window. Stop.
Click Window Button > (alt 1) :::: Close the Window and Quit the Application (e.g. calculator)
Click Window Button > (alt 2) :::: Close the Window and Hide the Application (e.g. iTunes)
Alt 1 and Alt 2 are at the discretion of programmers to
help people who probably should have quit or used hide because closing the last window wouldn't serve much purpose.
Clearly, you are not interested in learning OS X, so I'll leave that up there for users who might be.