Read the article. Apple doesn't want to replace what Bluetooth does with NFC, they (might) want to do what NFC does with Bluetooth. Less chips, cheaper design, cheaper device. About the only thing NFC offers over BT is passive communication, which I think most of us would prefer our phones don't do anyway.
If you were a merchant and you could buy an NFC payment system and get the Android people, or you could buy a BT one and get the Android people (Android phones have BT already) AND the iPhone people, which would you do?
Bluetooth is ill-posed for touchless payment as the communication range is too large. Imagine if you can pay with your credit card from 100m away, would you do it? The nice thing about NFC is that it provides a similar interface as a face-to-face communication (the communication range is 10cm) so it is much more well-suited for payments. The fact that you pay through your NFC means that you're present at the payment station. The 2 technologies are different and they do different things. Data rate over NFC is very low, so it is used only to transmit small data (e.g. contacts) or set up other types of communication (e.g. Bluetooth, WiFi). I seriously doubt that Apple would forsake NFC, they probably would include both technologies, as Android is doing.