Unlike a medical X-ray, the TSA X-ray machines are lower-energy beams that can only penetrate clothing and the topmost layers of skin. But according to the UCSF professors, the low-enegy rays do a "Compton scatter" off tissue layers just under the skin, possibly exposing some vital areas and leaving the tissues at risk of mutation.
When an X-ray Compton scatters, it doesn't shift an electron to a higher energy level; instead, it hits the electron hard enough to dislodge it from its atom. The authors note that this process is "likely breaking bonds," which could cause mutations in cells and raise the risk of cancer.
Dr. Holdren passed the letter on to the FDA for review. But, in the FDA's response, the agency cite five studies in response to the professors' request for independent verification of the safety of these X-rays; however, three are more than a decade old, and none of them deal specifically with the low-energy X-rays the professors are concerned about. The letter also doesn't mention the FDA's own classification of X-rays as carcinogens in 2005.
ARS technica: http://arstechnica.com/science/news/2010/11/fda-sidesteps-safety-concerns-over-tsa-body-scanners.ars