Principate
Saint Titanfall
IP is from The Pokemon Company (Nintendo, Game Freak, and Creatures). Not directly Nintendo. Nintendo is a part owner of Niantic (along with others - such a Google). Nintendo are making money because they have different involvement in some many areas.
Apple are making 30% on all IAP sold on iOS. They could probably be making more direct money from this that Nintendo are.
The game is obviously helping the Nintendo brand regain traction in the long run though -- which could be more helpful than anything else.
Nintendo actually owns and good chunk if not most of the IP's on the pokemon themselves, of the 3 partners they have the biggest stake overall when you get into the nitty gritty of it.