Just 3% you get, but not just from the Apple store. Now you can also get the 3% savings from a couple of other merchants such as walgreens and uber.
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3% using apple pay in the Apple Store and select merchants such as Uber or Walgreens, 2% using apple pay elsewhere and 1% using the physical card anywhere (including the select merchants that would otherwise give you 3% when using apple pay). Also note that any Apple Stores located in countries where Apple Pay hasn’t officially been released WILL NOT ACCEPT ANY FORM OF CONTACTLESS PAYMENT EVEN IF CONTACTLESS IS A STANDARD FORM OF PAYMENT IN THE REST OF THE COUNTRY WHERE THEY ARE LOCATED, and therefore cannot accept apple pay.