I actually used to sell payment processing services to small businesses, so I know pretty well what the costs were for it, and while the equipment itself was indeed costly, it was also an ongoing cost to the business.
Of course in this day and age where most people hate to carry cash and prefer to carry only a debit or credit card, it can mean a lot of lost sales to not accept a card, so it is a fine line stores have to balance when they consider what payment options to accept. The minimum purchase is to ensure they actually make a profit from the sale, if you buy a pack of gum and pay with a credit card, the store isn't likely to keep much, if any of the transaction.
That's why a lot of small businesses won't take credit cards, only cash or checks and some require a minimum purchase if they do take credit cards or may charge extra to use one. The customer doesn't see it, but Paypal definitely takes a cut and it's not unlike Valve's cut for when you buy something in the community market. All of those will charge a percentage of the purchase and sometimes a fee on top of that to purchase it.
Any time you use a credit or debit card the payment has to be processed via a payment processor, whether that is Paypal or another company that does it.
