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.
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.