I’m sure that while Cook is encouraging the little guy to boycott Indiana, he is more than happy to make as much money off of Indiana as he possibly can. If he were serious about his “principles”, he could just refuse to sell Apple products in states that he thinks are at odds with them. At the very least, he could close all Apple stores in those states. But, hey, that would cut into his giant paycheck, wouldn’t it?
I suspect there's a lot more money changing hands over this in DC than there would have been in Indiana.