I think there are a few problems with FaceTime.
First, there's a bit of a trend toward somewhat less interactive conversation. If text messages are rising in popularity as phone calls wane, it would also make sense that FaceTime wouldn't be the most popular. Plus, with FaceTime, you might not want to use it on a saturday at noon when you're still disheveled in your pyjamas.
Second, it only works with other Apple stuff right now. AT&T announced that they wanted to push for a video calling standard. I hope that the industry really coalesces. That will probably mean Google adopting FaceTime for Android handsets and Google Talk/Google+. Even if I have an iPhone, only one other member of my family has an Apple device. Many of my friends have PCs and Android handsets. That limits how important it can become for many people.
That said, my friend's grandmother loves it. She's too old to travel, but can see her grandchildren 4,000 miles away with it. It's really special for her.
Still, it will remain a bit more of a niche product since there isn't broad compatibility and, at least right now, there might be a stigma to using it when one doesn't feel put together.