My understanding is that the profits are accumulated in a cash/low-risk investment reserve, which serves several purposes: hedging against the ~100B of debt they apparently hold, ensuring smooth operation in a downturn, and also enabling the acquisition of valuable companies or talent, such as P.A. Semi in 2008.
Let's put it this way: it would be a lot harder for Apple to do what it wants if it didn't have a stupendous amount of cash to fund it. That money pile means that they can shoulder the risks of their own plans, and the fact that they just pile on more and more profit every year just means these plans are largely successful.
You perfectly articulated my reaction to all of the complaints. It seems like people believe companies should aim for as close to zero profit margin as possible, as if margin is immoral waste akin to greed, and not fuel for for the business.
Its not that it is immoral, just that it indicates management lacks the imagination of what to do with it which can be problematic if it is a competitive industry.