McDougal worked under Ron Johnson who built Apple's retailing empire (with much help from Steve Jobs). Johnson left to run JC Penney at the end of 2011. Since then Apple has struggled to fill his vacancy.
It initially hired John Browett to run its stores. That hire turned out to be a dud and Browett is gone.
Apple has been looking for months for someone to fill that position. If we had to guess, we'd say McDougal was probably passed over for the top job for a second time and decided he was ready to move on from working at Apple and not being given an opportunity to move up.
Apple confirmed McDougal's departure to various news outlets. Jim Bean, who was a VP of Finance is moving to take over the spot left by McDougal.