In their award, the Apple board of directors said (via Cnet) the pay is based on "Cook's performance in assuming responsibility for the company's day-to-day operations during Mr. Jobs's prior leaves of absence. The Board also took into account the 10-year vesting period of the award, the importance of retaining Mr. Cook, and the opportunities Mr. Cook would likely have if he were to seek other employment."
Cook was previously the COO under former CEO Steve Jobs and took over his role all three times Jobs was forced to take medical leaves for his cancer treatments and his liver transplant.
The compensation package is not the first for Cook, who was given 1 million restricted shares of Apple stock that vest in 5 years. At current value, those shares are worth over $400 million.