About Apple Pay for merchants
https://support.apple.com/en-us/HT204274

Are there additional fees to accept Apple Pay?
No. Apple doesn't charge any additional fees.
Apple pay不會收取任何額外的費用。

應該就是信用卡行動化。跟一般信用卡消費一樣，只有發卡銀行及商家之間的費用。(撇除不開發票的店因信用消費要額外收手續費的情況)