Maybe because it's not really a mature product. I just did Apple Pay at Whole Foods and it was a less than expedient process. It took a couple times to initiate, a couple tries on the thumbprint, had to enter my phone pin, then I had to sign because the guy said it was over $50 ($62.72). Whole thing took about 5 minutes. Luckily the folks behind me didn't mind a bit, they had their whole weekend free to wait for me.
Strange. My first time at Whole Foods a couple of days ago was super smooth. Only took once to initiate, one time with the fingerprint, didn't have to enter my phone pin (not sure why you had to?). Still had to sign though (let's face it, you can't leave Whole Foods without spending >$50/a small fortune). Only took seconds.