From Tim Cook’s memo, as published by Re/code:

This case is about much more than a single phone or a single investigation, so when we received the government’s order we knew we had to speak out. At stake is the data security of hundreds of millions of law-abiding people, and setting a dangerous precedent that threatens everyone’s civil liberties. […]

Our country has always been strongest when we come together. We feel the best way forward would be for the government to withdraw its demands under the All Writs Act and, as some in Congress have proposed, form a commission or other panel of experts on intelligence, technology and civil liberties to discuss the implications for law enforcement, national security, privacy and personal freedoms. Apple would gladly participate in such an effort.

Also worth reading: Apple’s frequently asked questions regarding the situation.