This article and its headline are misleading. No one is being "punished" and no one's pay is being "cut". All that happened is that 2015 was a blowout year and 2016 was (by comparison) not, so the exec team got a lower percentage of their target bonuses. From the actual filing

   2016 net sales and operating income were
   96.4% and 99.5% of the respective target
   goals set by the Compensation Committee.
   This performance resulted in a combined
   payout at 89.5% of target for each named
   executive officer ... the 2016 payouts to
   our named executive officers were significantly
   less than the annual cash incentive payouts for
   2015, reflecting strong pay-for-performance alignment.
   The Compensation Committee determined that no downward
   adjustments to the payouts would be made, based on
   Apple’s 2016 performance and the individual
   contributions of our named executive officers.