No, that's not what the article says. What the article says is that if you subscribe to Prime and purchase a certain amount, type, and quantity of goods in some configuration you might cause Amazon a loss.

If you subscribe to Prime in any other way, Amazon might make less profit, but you're not costing them money, you're 'feeding the beast.'

As others point out, those “losses” are more than made up by the customer lock in effects and market dominance they bring.

A sale on item “x” is not a loss if it’s net effect is to bring in massive profits. If there was no overall monetary benefit to prime it would be peculiar for Amazon to keep it.

Maintaining monopoly power > losses