They don't.
----------
Apple and MS have equally generic names for their products (since "window" doesn't always refer to physical glass), so one of them can't be right while the other is wrong.
Yes, actually it can. Since you admit Microsoft doesn't sell "Panes of glass" and Windows is not a synonym for Operating System, then Microsoft did not in fact trademark a descriptive term.
- App Store - Store that sells Applications. Exactly what Apple has
- Windows - Panes of glass or alternatively, in computing, a UI element that represents part of an application in Graphical environnements. Microsoft sells an Operating System.
Microsoft doesn't hold a trademark for Windows over panes of glass or specific UI elements. It hasn't sued Lowes for selling Windows for your house renovation needs nor as it sued Apple or Oracle or HP over using Windows in their Graphical environnements, be it Finder or CDE or the Java Desktop System. It hasn't sued MIT over the X-Window System, or asked that XCreateWindow() be removed from xlib, that Apple do away with UIWindow or NSWindow in their respective UIKit or AppKit frameworks.
That is how it is different. It's also something we've explained already. Again. And again.
- App Store = descriptive
- Windows = generic word
- Apple = generic word
- Google = generic word
You can trademark a generic word, but if it is descriptive, you have to show it has achieved Secondary Meaning. See legal definition for that, I posted it earlier.