The iPhone 6 and 6 Plus definitely have NFC functionality, as was confirmed on-stage during the presentation of Apple Pay, but when it comes to using the chip for anything other than Apple's own payment system, it really doesn't have near-field capabilities. As Cult of Mac confirmed with Apple, the NFC feature on Apple's new phones will only be used with Apple Pay, and developers won't have access to the feature for their own apps.
This of course could change in the future, just as Touch ID will soon be opened for developers to utilize the ID verification feature in their own software, but at the moment it is indeed being locked down.
Apple's relationship with NFC has been a long and complicated one. In short, the company has taken heat year after year from a small number of vocal critics to bemoan its refusal to embrace the technology, while at the same time Apple has shown consistently that it really didn't need to do so. Had Apple included NFC early on, especially for some type of payment system, it would likely have aided competitors (namely Android manufacturers) by giving retailers more reason to include NFC payment kiosks in their stores. Apple Pay is sort of a workaround, so it's not entirely surprising that third parties won't have access to the hardware functionality right from the start.