Samsung Pay was introduced with the new Samsung flagship devices. This service was just the same as Apple Pay and Google Wallet. They acquired LoopPay and with the help of their services, they made the Samsung Pay service.
They made their service compatible with the Magnetic secure transmission. So now you were able to pay at terminals which otherwise would require to swipe your magnetic credit or debit card.
Now it seems like once you root your device, the service stops working. The Samsung Pay service will stop to work because the integrity of the system is compromised.
Features like KNOX will also stop to work. This is because the Samsung Pay heavily relies on security and once security is out of the equation then so is Samsung Pay.
Once the Xperia Z3 is rooted, we’ve heard that the camera quality becomes very poor so this type of thing is common in rooted devices.
If you want to use Samsung Pay, do not ever root your Galaxy S6 or S6 Edge.