Why does pressing the red X close some windows, and seemingly minimize others?
Mac OS has always had a multiple document interface. Applications like TextEdit can have multiple main windows open without requiring multiple instances. The open command doesn't usually open documents over the current document.
The close button might also quit the application after closing the last window like on Windows. But what if you want to create a new document? Many applications create an untitled document on startup. Should closing it quit the application?
There's no real harm in keeping applications running in the background. They don't usually use CPU, and you should have enough free or inactive memory anyway. Quitting and opening applications all the time would take more time. OS X has also supported automatic termination since 10.7.
The close button does actually quit some applications with a single main window, like Dictionary, System Preferences, and Calculator. Opening them again doesn't take that long and quitting them frees users from having to do it manually.