FaceTime is Apple's video chat application that runs on a variety of its products including the iPhone. One of the great things about the Internet is that in principle it shouldn't matter what sort of traffic goes across it - that is all defined by the programs that communicate across it using a very simple protocol.
This is a very non-telco way of thinking and there has been great resistance along the way. Network neutrality is something of a catchphrase that means many things to different people, but in general it usually is taken to meaning that a carrier can't restrict content, sites, platforms, services and so on... The network must be neutral to these things. The devil is into details and the rules that finally made it through are heavily flawed from all points of view. For example - the level of network neutrality on physically wired connections (like fiber, dsl or cable based connections) is more rigorous than that over cellular networks where it doesn't really exist. The language speaks of unreasonable discrimination being prohibited - but again it specifically only applies to fixed broadband providers.
AT&T only allows iPhone FaceTime if you have one of their higher end data plans - it simply isn't allowed on the basic data plan. Similarly the device you can attach a data plan to is restricted - you have to buy and extra service if you want the connection you pay for to be shared with other devices you own (imagine your cable company billing you for each PC that connects to your home network for example). Such actions clearly violate the spirit of network neutrality, but not the FCC's curiously named Open Internet Rules which make it clear they only apply to the fixed broadband providers. (and even then it is watered down).
People have been upset with AT&T over its decision (note - Verizon allows you to use FaceTime on iPhones on their network so, by this measure and a few others, the link they offer is more open and more neutral than AT&T's, but it has issues of its own). Papers of intent have been filed with the FCC petitioning them to have a hearing and rule on the matter (via the Verge). It appears the FCC will take up the matter... but given the nature of the Open Internet Rules as it applies to cellular service I'm not expecting a ruling favorable to those who value the concept. The real battle for network neutrality was lost a few years ago and it seems unlikely that it will be revisited anytime soon.
There is a possible chance something will be done though as this ruling does discriminate against a minority - specifically the deaf who use products like FaceTime to communicate... So we shall see ...