Customer USD -> Customer BTC: 1% + $0.15 (Coinbase)
Customer BTC -> Merchant BTC: $0.06 (transaction fees, currently abnormally high due to price spike)
Merchant BTC -> Merchant USD: 0.99% (Bitpay)
Total: 1.99% + $0.24
Compare: credit cards and Paypal (2.9% + $0.30)
So even there it works out fine.