Some merchants already are, though. For instance, Kroger and Walmart Pay being promoted (which can eventually lead to moving people off the card rails onto ACH or similar), not to mention Kroger disabling Visa credit support at a few of their brands. Plus the many smaller businesses that have minimums and/or surcharges for card use.
I don't think it's the belief that they'll pay extra for AP (though in some circumstances they might pay extra for contactless debit card transactions if they end up routing over Visa/MC instead of a domestic debit network). Rather, it's the prospect of card use in general increasing when using a card becomes easier. If you're already unhappy at paying the 3% or whatever for the card volume you're getting, I can see trying to prevent or discourage that from increasing.
On the other hand, if merchants only have to pay, say, 2.5% instead of 3% for contactless, that might be enough of a savings for the holdouts to make it worthwhile to enable. Of course, I don't see Visa/MC ever doing that so this is somewhat moot, but still.
Switchover by merchants to machines that have NFC readers. This has been the chicken or egg problem. Since there was no initial consumer demand to use Apple Pay, and merchants had already purchased machines with chip readers to accommodate the new credit cards, merchants didn't have a reason to rush out and buy new machines just to add NFC readers. This was true for small merchants, e.g., my dry cleaner, but also for large merchants like Lowe's who still haven't invested in new NFC capable machines. Adoption of the NFC capable machines has grown steadily, but is still a cost issue, so they aren't ubiquitous. Witness Costco who now accepts Apple Pay at all its stores, but hasn't switched out the reader on its gas pumps, so you can't use Apple Pay to purchase gas.
Note that a lot of the holdouts have hardware that's perfectly capable of NFC (for instance, Lowe's uses the same Verifone MX925s that Target uses). Their POS software, assuming it's not 100% custom, might very well support contactless too (but might also need enough retailer specific changes such that it triggers recertification--which again, might not be worth the hassle unless they can get a cost savings and/or more customers).
Many of the holdouts already have loyalty programs or other mechanisms to get that data. They could just vastly increase marketing/incentives for those to make up for any losses in data from using contactless. Hell, Kohl's and Starbucks have their own payment apps too, but still allow contactless payment in store.
This might impact Apple Pay specifically, but contactless cards may very well be more popular. The few that exist at the moment supposedly already have double digit transaction volume on the contactless interface. (I can't find the source for that at the moment.)
