In my (not aviation related) business I charge the customer 2.5% for using a credit card, no charge for debit cards.
In reality I do actually make a very small profit over the year on my credit card charges but this is offset by the small losses I make by not charging for debit cards.
There are other implications to consider.
Some card companies charge the business more than others and a small business simply doesn't have the resources to calculate the charges on an individual basis.
When a business takes a credit card payment, it is accepting some risk as the funds into your bank account are by no means guarenteed; payments can be recinded by the customer or refused by the paying bank.
Charges are calculated on transaction value, not profit. So, if I charge a customer £100 but my material costs are £90.00 and he then pays by credit card the card company will pocket £2.50 of my £10 profit which equates to 25% of the profit margin. Not good for any business.
When a customer pays by credit card, he is in fact paying for insurance on the purchase as all credit card transactions are protected by law in this respect and it's reasonable to expect that insurance to come at a small cost.