According to 9to5mac.com, just as they do with iOS Personal Hotspot features, AT&T looks as though they will control and charge for FaceTime over cellular with iOS 6. This feature in iOS 6 means that customers have more flexibility with FaceTime as they can use it anywhere.
AT&T to charge iPhone users for using FaceTime over 3G
AT&T recently said that they are working with Apple on the developer build of the operating system and will let customers have more information when it becomes available.
When they tried to get the same error message on enabling FaceTime over a cellular connection on the iPad the feature did enable without showing any issues. AT&T charges customers separately to use the Personal Hotspot on their network and it seems that they will do the same when using FaceTime in particular over a cellular connection.
Thanks to the large amount of data that would be used when making a FaceTime call over cellular there is no wonder that AT&T will want to charge their customers to use this feature. At the moment iOS carrier plans are unclear and AT&T is the first carrier in the US to show evidence in iOS 6 beta 3 that they will charge customers to use this feature.
iOS 6 is expected to roll out at the same time as the release of the iPhone 5 which if rumors hold true will be before the end of the year.