I wonder about that. I'm sure they're selling your data too, but I wonder if the kickbacks the retailer gets for your data is actually comparable to the discount, or if their incentive is just the "loyalty" - convincing you to spend money you wouldn't already spend and to default to them instead of trying alternatives because you want the points or you're close to a reward.
They seem like a pretty natural successor to the punch card model, which I can't imagine had a motive beyond the obvious.