Also keep in mind that the phone and reader need to be really close for the NFC transaction to work - close as in one to two inches apart. So simply walking by an illegal scanner won't do anything. And most clothing, purses bags etc offer more than enough shielding to block the signal as well, so your phone needs to be out and placed close to the reader.
Also note that no transaction can occur until you authorize it with your fingerprint or screen lock passcode. It is not a passive process - you must authenticate for each and every Apple pay transaction.
As for the communications, they are as secure as any credit card transaction. But with the added benefit that the vendor your shopping at actually never has access to your actual credit card number or CVV. Vendors are blind to the system and only know whether the charge gets authorized or not.