The subject of this story is both a user and a customer. But apart from cases (like this one) where the advertising is for political campaigns, the goal of advertisers is to sell products to facebook's users. So instead of being customers of Facebook, they are customers of Facebook's customers. The money trail simply has an extra step in the middle. There are surely be some nuanced differences in that more-complex relationship, but overall the motivation for facebook is the same as if they were trying to sell their own products directly to users, which presumably they do sometimes also. Though they probably have to deal with a higher risk of antitrust accusations when they operate that way.
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