Matt, I had the same thing happen to me. My iMac, MacBook Air, iPad Air, and iPhone 5S all seemingly had the Phone Cellular Calls option disappear. No trace in the FaceTime preferences in the Macs or the iOS devices.
I fixed this by doing a complete restart on the iPhone (e.g., hold down the Power and Home keys until the white Apple logo appears). Once the phone came back on-line, the iPhone Cellular Calls option appeared in the FaceTime Preferences. I did a reset on the iPad too and the option came back there as well. Once the phone was reset, the cellular calls option also magically appeared in the Face Time preferences on the Macs (all devices signed into the same iCloud account and on the same Wifi network).
So do a restart on your phone. Hope this helps others as well.