+ 1 million, lol
Unless you're squatting wide and sitting back (PL squat or box squat) then you should go ATF. Paralell is a rule in powerlifting, nothing more. If you're NOT training for a powerlifting competition, then you're half squatting at paralell and anything higher is even more laughable.
ATF is safe when done right, stress transferred from the knees to the hips as Sarge said. The only time ATF squatting can cause problems is with douche bag form, usually caused by people using too much weight (ie, what they "squat" over a 6 inch range of motion) as CS said. The flexibility comes over time.....another big problem is people using too much weight, doing half or quarter squats and assuming they'll eventually be able to get lower as they add weight......start out all the way and work up from there