Here's a post from DKDonkeyKong that explains the problem:
I just got my new Gold iPhone 6 Plus (128GB) yesterday. I went to McDonalds, excited to purchase lunch using my new device. The lady at the front gave me my total, and I said "I'm going to pay using my new iPhone". She immediately gave a very confused look and told me I could pay using cash or credit. I said that Apple Pay is an NFC-based feature and should work with any NFC terminal. She told me to wait just a moment while she spoke with her manager. At that point I was rather embarrassed and told her I'd just pay with my card.
Other people have been having the same problem. One forum poster said "I have stopped even trying to tell anybody I want to use Apple Pay. They just get confused and it holds things up."
iPhone 6 users have hit upon a way to get around this, though. They recommend asking to pay with a credit card, and then secretly using Apple Pay without telling the cashier.
Here's some advice from a forum user on how to use Apple Pay in McDonald's:
Do NOT involve the cashier. While they ring up, I generally have my phone near the terminal [with] home button pushed. This works over 50% of time. For those other times, when they ask cash or credit, simply say credit. People spend too much time talking to the cashiers. They're easily confused.
Another forum user says "Don't confuse a McDonald's worker with the facts!! Just hold the phone up to the reader. Worked fine for me."
Other advice given to people wanting to use Apple Pay at McDonald's includes "Keep your mouth closed" and "Don't bother even telling them."
This could become a problem for Apple if major retailers don't train their staff in how to use Apple Pay. The whole point of the system is to make paying for things more simple. If Apple Pay is causing delays in lines at the checkout, or if retail employees don't know what it is, then people could stop using it.