Which is not to say that there aren't shenanigans going on, but there's a reason that consumers really like MasterCard and visa, they both look after customer interests, sometimes at the expense of merchants.
IE, CC companies offer their customers consumer protection to encourage use of their product. They charge merchants when a consumer uses the product. Then, they unload the risks, costs and other burdens inherent in offering this add on service onto merchants as well. This is why they put little effort into investigating claims, making it feasible for merchants to dispute them or otherwise preventing fraudulent claims. It's has a distinct odor of oligopoly.
Oligopoly also allows for price setting. IE, the forces pushing the cost of a good or service closer to the (marginal) cost of producing it are weak. It could also be that "card present" is cheaper because in-store purchases have to compete with cash purchases. IE, they might be charging the higher fees because they can, not because they have to.
This is the reason why pretty much nobody accepts swipe cards in EU anymore - there's very few places which even have swipe terminals, it's all chip and pin. The couple times when my chip didn't work, the cashier had to key in the number of the card manually, because she didn't have a swipe terminal at the till.