Pokémon GO is a massive hit for Niantic and The Pokémon Company. After just a few days, the game has rocketed to the top of the Play Store, including the list of top grossing apps. So, it's already making a ton of money, but it's going to be making even more in the not too distant future. Niantic CEO John Hanke recently noted that sponsored locations will be part of the game.
Players of Niantic's last AR game Ingress will be familiar with sponsored locations. Right now, most PokéStops and gyms are at neutral locations like statues, parks, and local landmarks. However, businesses will eventually be able to pay Niantic to set up PokéStops (and maybe gyms) at their physical locations. This would increase the number of people passing through dramatically, but the business would pay based on the number of people who interact with the game at that location.
Niantic says it will provide more information on sponsored locations later. It's not clear how many sponsored locations will be available or what will happen when they expire. A sponsored PokéStops would be straightforward—when it's gone you just can't get any more items there. A gym occupied by a team would come with added complications when a sponsorship ends.