You're assuming they won't start blocking other video chat applications. Carriers in a number of countries do just that.
As for why they'd want to charge vs. allowing people to exceed their caps, you're assuming that using Facetime after paying said fee won't still count against data. I'm not so sure.
About the only way I could see this being close to fair is if people had a choice: pay a small fee for unlimited Facetime, or don't pay a fee and have it count against data usage.