The problem is that recently, Apple seems more concerned with protecting its empire even when that conflicts with its brand. Combine this with the recent fury over Apple's App Store policies, and it's becoming clear that Apple is now that giant machine. As a result, it's done what no brand should ever do: betray the very values that made people love it in the first place.
I suppose you can sum it up with this statement from Apple's opposition to Prepear's application:
"Apple would be damaged by the registration of Applicant's Mark in connection with Applicant's Services because Applicant's Mark so closely resemble the Apple Marks that it is likely to cause confusion, mistake, or deception in the minds of consumers..."
No it won't. But picking unnecessary fights over a logo that no one will ever confuse with Apple will do far more damage in the long run. That's something every business should learn from.