He is wrong. In fact Apple charges the banks: http://www.bloomberg.com/news/2014-09-10/apple-said-to-reap-... Which makes sense, when you read the technical details published earlier today here on HN: http://clover-developers.blogspot.de/2014/09/apple-pay.html
The article you're linking to is not definitive. The source is anonymous and not confirmed:
"Under deals reached with banks individually, Cupertino, California-based Apple will collect a fee for each transaction, said one of the people, who requested anonymity because terms aren’t public."