Amazon gives non-Prime members free shipping at $35 or more of eligible items. Instead of simply letting users get the product with free shipping, they’ve added a discount that prices it exactly one cent below the $35 limit, while only subsidizing the price with $3.38, which is about half of what they’ll then charge you for shipping.
Non profit means no profit. Salaries, rent, etc are not paid from profit.
That is fundamentally what profit is, revenue less expenses. By definition, profit is money that does not have anywhere to go in a business, and so gets distributed to stake holders of the company.