At the risk of sounding like a jerk, why does Apple need to spend all their time worrying about historic buildings or other social issues when people are pissed off about the lack of focus on their products?
If you're going to make a presentation to a government body about renovations to a historic structure, you're going to try to impress them with your respect for history, architectural integrity, etc. It's a necessary part of the process.
Considering how passionate Apple is about matters like design, I don't doubt that they do respect the historic buildings they choose for retail locations. However, their ultimate purpose is to build attractive retail stores in upscale shopping districts. Whether those are original, contemporary architectural designs, or renovated historic landmarks is going to come down to location, local politics, etc.
The architects who designed the Carnegie Libraries built them, from the start, to impress the public with their importance - both the cultural importance of the free public library and the knowledge contained therein, and the personal importance and largesse of Andrew Carnegie. Outside and in, they were designed make patrons feel like they were embarking on a special experience.
Retailers of upscale goods also want to make their patrons feel that they and the shopping experience are special, and that the goods they're buying are special. However, if you're seeking approval from government bodies, "I want to make oodles of money" is not going to close the deal.
If Apple was hitting the ball out the park every day then I would say, go and use your money to give something back, but they aren't making products that I want any more and while I know the people fixing stores aren't the people designing products, this ship has no one holding the rudder.
In a company of Apple's size, there are many ships in the fleet, and many hands on many rudders. One can even argue that Apple is a navy, with multiple fleets. No navy will win every engagement. It may even sail past a heavily-defended or strategically-unimportant port in order to win a larger objective. The citizens of those bypassed ports may feel betrayed or abandoned, but the decision to not steer in their direction is hardly proof that there's nobody in charge of the navy.