What Tim Cook means is that there will be little use of physical currency in the future. We will only use digital currency in the future. Bitcoin is the best digital currency, so if it is used widely, Applepay will integrate it.
apple wont integrate anything. they are known to try to always make a new standard and let their customers feel elitist.
imho: google, paypal and wu may integrate bitcoin.... but apple? no ;-)
I think apple has absolutely no business in trying to come up with their own currency.. I don't see them becoming pro-Bitcoin given their strong centralized and closed source policy, so what I think that will happen is they will simply try to compete against Paypal using the goverment's electronic fiat.