That's a sufficiently vague and unsupported response.
Here's the more specific explanation from Cook:
Taxes for multinational companies are complex, yet a fundamental principle is recognized around the world: A company’s profits should be taxed in the country where the value is created. Apple, Ireland and the United States all agree on this principle.
In Apple’s case, nearly all of our research and development takes place in California, so the vast majority of our profits are taxed in the United States. European companies doing business in the U.S. are taxed according to the same principle. But the Commission is now calling to retroactively change those rules.
A "fundamental principle" is not a law. The Commission's investigation pertains to the taxes paid by Irish entities, not Apple Inc.
In addition, what Mr. Cook is saying is insincere. If Apple believed that its international profits should be taxed in the country where 'value' is created, then it should be funnelling them to Apple Inc. and paying the U.S. corporate rate, not through an Irish subsidiary and paying a virtually zero rate, and certainly not hoarding those profits outside of the United States.
There is nothing illegal with that particular arrangement (minus the illegal state aid regarding the very low rate), but it is at odds with what Mr. Cook wrote in justifying the low tax rate on profits earned through Irish subsidiaries. One the one hand, in justifying the zero rate in Europe, Mr. Cook says taxes should be paid in the United States. On the other hand, Mr. Cook says he won't funnel those profits to the United States because paying the U.S. corporate rate would not be "appropriate".
Mr. Cook is a hypocrite. If he wants to win this argument, then he cannot have it both ways.