What purpose would it serve to have an "innocent" person's prints on file? Well, are there applications that could protect against identity theft? What if someone using your information was scanned and didn't match?
Having said that, what bothers me more about this is that it isn't being used on everyone flying. It could identify many people (in addition to potential terrorists) that would be better taken into custody and could potentially uncover cases of identify theft, especially if broadened to include Americans. Given our large illegal immigrant population and issues around identity theft, I would support this, again if it was sufficiently accurate. Of course, this would require that we all be the first ones to submit prints so that anyone else using our identity would be compared to ours. Hmm.