Strange, I've been in IT for 20 years, and until Apple produced the App Store, I've never heard anyone in IT (or outside IT for that matter) use the word "app", let alone "App Store".
These things can be hard to judge with hindsight. However, I have heard many many people using the word "trouser", but have never, ever heard anyone saying they bought anything in a "Trouser Store". So I would say that a company specialising in selling trousers on the web could open a web store, call it "Trouser Store", and get a trademark for the name. And if they were successful with their store, then in three years time all their competitors would claim that the term is generic and everybody should be allowed to call their business "The Trouser Store".
Tell me how you can buy something from Amazon's app store and load it on an iDevice
Tell me how you can buy something from Apple's appstore and install it on something OTHER than an iDevice
So I ask - WHAT confusion?!
To your first point: Apple spends tons of marketing dollars to explain to people that they can go to the App Store and either buy apps or get free apps that will run on an iPod Touch, iPhone, or iPad. And some people _will_ go to the Amazon App Store, buy something, and then complain to Apple that it won't run on their iPhone. That's confusion.
Next, Apple has spent marketing dollars to tell people that they can go to the App Store and buy apps, and that Apple's app store is a good place to buy apps, and every time customers do that, Apple makes money. Now people will go to the Amazon App Store, thinking they are at the excellent App Store that is advertised by Apple, when in fact they are not. That's confusion.
Your second part is of course irrelevant because Apple _does_ have the trademark for "App Store", so if you were confused by Apple's use of the term, that wouldn't matter.
Ubuntu has had a Software Center long before Apple brought out the iPhone and wanted to control what people installed, then the transition to the desktop.
That would be a very good argument if Apple (or anyone else other than Ubuntu) tried to trademark "Software Center". The argument for Apple being allowed to trademark "App Store" is that the term "App Store" hasn't been used before Apple used it.