Unless you're 100% profitable, its always a higher effective %. If you're running somewhere closer to 10% (remember that it needs to be after all costs/paychecks/etc), that's nearly a third of your profit.

Anything optional that skims off the top cuts into profits extremely quickly.

I think this is the wrong way to look at it. If 3% fees mean a company is 7% profitable, it's 7% profitable, not 10%.

Businesses which accept credit cards get the business of customers who want to use credit cards. Those which don't, do not. Me? I want to tap my watch, get my 2%, and leave. I do not want to reach into my pocket, extract my debit card, and enter my PIN. Not a dealbreaker, I do business on the regular with two places which are cash and debit. But it's my preference.

Yes, there is an underlying coordination problem here. The major payment networks are quite probably engaging in anticompetitive behavior, as the lawsuit we're talking about indicates. But this does not, at all, mean that businesses which accept credit cards are penalized financially for that decision, on the contrary, in expectation we would find that most are rewarded for it, on the simple evidence that most of them do, in fact, accept them.

Separating it from any other costly incentive to do business, free samples, flyers, discount sales, loss leaders, is just special pleading. A cost benefit analysis includes costs and benefits, or it is unworthy of the name: and customers doing business are a benefit to that business.