Apple has already recruited many major stores before the Apple Pay announcement to ensure it was usable to some extent.
Apple didn't have to "recruit" those merchants. From the quick list I saw, they already have NFC terminals. And since those merchants don't have to do anything, it was a no-brainer to agree to be promoted as a "flagship" merchant.
Subway is the odd one out. The individual stores are typically operated by franchisees, and I'm not sure that Subway (the company) actually controls their PoS terminal deployment.
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I think you make a very good point here. Thing is, other competitors have already partnered up with merchants when this technology first came out so where does that leave Apple? I'd say Apple has a lot more work to do in gaining support for the Apple Pay. Or, could it be that merchants trust one phone manufacture over the others (e.g. Apple, Samsung, HTC, etc), and are willing to sign up going forward? Time will tell I suppose.
Apple's "partnering" with merchants is nothing more than cross-promotion. To a merchant's Point of Sale terminal,

Merchants don't have to do anything special, other than to add the NFC option to an EMV terminal (that they already have to buy before 10/2015), or enable the NFC functionality.