I think media likes to blow things out of proportion, when they don't understand the specific patents or trademarks. Apple has trademarked its Apple logo with the leaf, just like Mcdonalds trademarked the "M" logo, Louis Vutton with the "LV" logo. Shell has a trademark for its "Shell" logo and Yahoo has a trademark for its letter "Y" logo. All major companies trademark their logo symbols. There's nothing wrong with that.
This is okay. A consumer would be confused if two gas stations used the same logo. If they liked Shell, they wouldn't know what to trust!
Regarding the joke about patenting a rectangle, read the entire patent's complete description on the FCC page. It's not only a patent for a rectangle. It's a design patent for the device itself including home button layout and general shape. There are still tablets that are rectangular, but they shouldn't infringe upon the specific design of the ipad. The older galaxy tabs looked very similar, but recently, their newer designs are different. Patenting device designs is not new. Nintendo has design patents for button arrangement and controller designs.
This is ridiculous, as Apple's placement of these elements is an optimal design. Why rounded corners? Because sharp edges get caught on things and provide stress points for breaking the glass. Why home button in centre? Because it's placed at a good position for the thumb. Why bezel? Because otherwise hands would cover the screen. These are all obvious things, and are where technology would go Apple-or-not, so why should Apple be able to restrict the next level of technology advancement to their own company? Oh right, because the patent system is stupid.
Fashion companies have design patents on their perfume bottles and much more. Apple's iconic store brings in billions of dollars for Apple and it's a major company strength. Millions of users visit it every time. They want to keep that to themselves. Other major retail chains also have patents on their store designs too specifically big fashion companies. Some of the technology that Apple has developed includes single slabbed curved glass that they've used for some of their glass stores and are using it to build the outsides for the new spaceship styled campus.
Apple's store design isn't actually all that iconic, as it has parallels to a fashion store, but in white. In any case, without the Apple logo (which I'm okay with trademarking), it's not an Apple store, so there should be no problem with this.
You always hear the media blabber about Apple getting patents. Yet all companies have trivial patents. They may seem trivial to you, but for them it is worth a lot. Amazon has the "one-click buy shopping cart" patent and Google has a design patent for their homepage "consisting of an input box with a button." Google also has design patents on their server enclosures and much more. Microsoft also has similar trivial patents. Design is one of the biggest strengths for Apple and Apple knows this specifically. Apple's design patent for the store in its entirety. I'm sure companies will have similar interiors, but if the design mimics the Apple store to a large extent, then it will be a problem.
These trivial patents are "worth a lot" because they're trivial. They're so general that the companies that patent them can basically apply a licensing fee to anything that irks them the wrong way.