Ignoring advertising for a moment, mobile apps are first-class clients, whereas mobile websites frequently aren't. Mobile websites are usually stripped-down experiences, and the company doesn't want to invest the effort in turning the mobile website into a first-class client because most of the users are on the mobile app. It's easier to just funnel people into the app, which is also much more likely to get the user to come back (now they have the app on their home screen, the site can send notifications, etc)