In fact, Apple's own 2012 proxy statement filed with the U.S. Securities and Exchange Commission states that Cook's compensation should be viewed "over the 10-year vesting period and not solely as compensation for 2011."
Then why does this article even exist? (and also as noted in the CNN/Money magazine article)
If the total stock compensation is included, Cook's earnings in 2011 were well beyond second-place finisher Larry Ellison of Oracle Corp., who made $77.6 million last year. In third place was former Apple retail chief Ron Johnson, who made $53.3 million in his new role at U.S. retailer JC
Then based on the same reasoning as the article, in 10 years, Larry Ellison, Ron Johnson and Philippe Dauman will have made far more than Cook (based on current salaries). $776 million, $533 million & $431 million respectively.