Maybe I've spent too long in Quaker churches, but every stranger should be treated the same, and this element of business has a moral valence.
This is probably the most approaching explanation of what's going on here. Basically, if they think that, statistically speaking, you're more lucrative as a customer, they'll treat you differently. I understand the motivation for it, but I feel all that reasoning is defeated by the standard argument for universal pricing (and is, in some ways, the same thing – many companies charge for faster support responses).
Don't get me wrong, I like being loyal to local stores, particularly restaurants, and sometimes, for small places, they'll throw me a free thing – I'm uncomfortable with it, but it has happened. But the scoring of it removes the "element of the community" element of actual loyalty. Rewarding loyalty seems potentially pro-social, but this isn't that.
Perhaps the headline seems a bit strong, but they are prejudging you, and it is done at an institutional level. Any principled opposition to institutional prejudice ought to at least grudgingly admit this is bad.