Please look up what 'amnesty' means. Apple isn't doing anything wrong or illegal by keeping its cash outside of the US. Also note the the US tax code is the only one (in advanced countries) to try to tax earnings made outside of its jurisdiction (e.g. for earnings made in Japan, and already taxed locally there).

Cook is not saying Apple shouldn't pay taxes, he simply says the IRS has no business taking 40% of earnings not made in the US. If you were an expat you would strongly agree with him.