It's still more secure at a place like TJ's because of the existence of credit card skimming devices which can be installed on all kinds of credit card terminals. So it would be even more secure at a place like that because of the encryption they use.
And actually, I really doubt Apple Pay will be something most hotel chains will ever adopt in its current form. Hotels need the ability to charge your credit card at a later time in case you trash the room, raid the mini bar, etc. With Apple Pays current implementation, I'm fairly certain they wouldn't be able to add an additional charge to an Apple Pay transaction due to the handshake method currently in place.