That's because up until recently credit card companies required merchants to charge the same prices. They had the power to do this because they are basically a cartel.

But yes, you're right. You would be paying twice, just like you're still paying once even if you pay with cash. This is a real problem, but it's not an inherent flaw in cryptocurrencies, IMO. Just a practical consequence of our existing financial system. That doesn't make it any less real, but it's "not Bitcoin's fault" so to speak.

And if I pay in cash I'm also paying the baked in credit card cost.

Rationally one would think that if some cryptocoin did see large scale adoption then it would have the same effect as credit cards where the consumer doesn't actually see the transaction costs.