It's up to the businesses that operates the rewards program to make then available. There are two possible ways the the retailer can make rewards card available. They can add them to wallet/passbook with a scan code. If their CC terminal will support it, the information can be passed using NFC (Walgreens offers this).
Apple does not support all of the possible bar code types in Wallet/Passbook, so companies like CVS that use a UPC type can't add theirs.
Walgreens is the only one that I'm currently aware of that offers the capability to send your rewards information to the POS using NFC.