Apple had tried to fight the request with the argument that it would "cumulative and duplicative" since 11 other Apple executives had already been questioned. Unfortunately for Apple that argument did not hold water.
The judge ruled that the CEO was a valid witness, and given that Steve Jobs had died before Apple's misdeeds were brought to light it made sense to question his replacement. Judge Cote cited the death of Jobs as a key reason in ordering the deposition: "Because of that loss, I think the government is entitled to take testimony from high-level executives within Apple about topics relevant to the government case," as well as to counter Apple's defense arguments, she said.
Apple is the sole remaining defendant in an anti-trust lawsuit that was filed last year. Their 5 co-conspirators, Macmillan, Penguin, S&S, HarperCollins, and Hachette have all settle with the US Dept of Justice as well as the similar lawsuit brought by some of the US states.