This isn’t the issue from last fall, but Apple addressed questions regarding FaceTime security to ZDNet. An Apple representative assured the site that the FaceTime conversation stream is encrypted from end to end, and each FaceTime session has unique session keys for each user.
What this does is make FaceTime HIPAA compliant as long as the wireless network being used utilizes WPA2 Enterprise security with 128-bit AES encryption. HIPAA (Health Insurance Portability and Accountability Act) is the U.S. standard for electronic health care transactions designed to keep these records secure and protect patient privacy. With the protocols being followed, those in the healthcare industry can apply for grants for Apple gear since HIPAA compliance is required.
Source: The Unofficial Apple Weblog (TUAW)