This is an opinion, but I think it has more to do with the market's uncertainty about the long-term future of the company without Steve Jobs. Apple hasn't released anything more than incremental upgrades to its existing product lines since Jobs passed, and while some people would argue about the Apple watch, Jobs played a significant role in its development prior to his death, so that doesn't really count.
Whether you like or hate Apple, you had to admire Jobs' passion and creativity, and there's real question as to whether the company can sustain its dominance in the market without the Jobs vision over the long haul.
My guess is that the market is leaning slightly toward the "no" column, but only ever so slightly. The company continues to deliver fantastic results, but how long will that last of their next products don't wow consumers the way previous ones have? This skepticism manifests itself in a stock that trades at a lower P/E than it deserves to, but this is just my opinion.
I hope this helps.