I dare you to develop an OS, call it Windows (sans the "Microsoft" part) and see what happens.
Ditto another completely generic brand name, Office.
You're actually proving the point against yourself.
MS Office products are only trademarked within their own specific context.
Notice that in the case of Microsoft Office, only the logo itself is trademarked:
http://www.microsoft.com/about/legal/en/us/IntellectualProperty/Trademarks/EN-US.aspx
Same deal with Word. Only the logo is trademarked, not the name, because it's too generic.
However, PowerPoint, Outlook, and Excel are all trademarked names, because they aren't generic.
I have OpenOffice running right now on my macbook pro. Are you going to try and tell me that Microsoft owns the second part of that product name?
They are only able to have a trademark registration on Windows because it doesn't specifically have anything to do with, well...windows. Like on a house or a car or an airplane. Unrelated.
Kind of like Apple can be a trademarked name for a company that sells computers. Nobody is confused about the fact that Apple, Inc isn't selling produce.
App store is a sufficiently generic term that Apple is going to lose this decision in the end. They pretty much have to defend the trademark in the mean time, but it's a lost cause.