I wish I had charts and graphs and historical data to support my opinion. Heck, I wish I had some credible background, but I don't. Nevertheless, to me the reason Apple decided to charge $0.99 for FaceTime is simple and smart. They are after first-time app store buyers.
The money that Apple will make on FaceTime will be insignificant compared to the follow up purchases which will result from the influx of new users this will bring to the platform. Given how seamless Apple has made their App Store, and how much content is available, their main challenge is getting people to go through the process once and making sure they have a good experience.
This isn't just about getting people to sign up for an account and provide a credit card though. A lot of people already have that setup thanks to their iPhone/Touch. This is about getting first time buyers to feel like that App Store is a place to get good value. Reviews are already saying it's totally worth it. By charging $0.99 for a high quality and practical application, Apple is making sure the a user's first experience with the App Store is positive in every respect.
I might be an extreme case. I haven't even launched the App Store. I don't have an App Store account. Yet even I'm considering buying FaceTime. I mean, it's 0.99$. I'd be stupid not too, right?