Caveat #1: There is no completely safe dose of radiation. You can't fire a bajillion high energy photons at millions of people and expect no damage to be done.
Caveat #2: I'm not a doctor, radiologist, or epidemiologist, but the relative risks (as far as I can tell) suggest to me that the probability of being significantly harmed by a TSA scan are somewhere between winning the lottery and being struck and killed by a meteorite.
Now to get to the blogpost in particular, it's based primarily on the letter of concern written by researchers at UCSF. Thus, it is relevant to link to the FDA's fairly authoritative response.
Experts can and should continue to discuss, explore, measure, and hammer out all of these issues, but I want to address a few particular points from the blogpost.
#1: The scanners preferentially deposit radiation in the skin, thus 'concentrating' the dose in one particular part of the body.
This is true, but the effect has been taken into account. The National Council on Radiation Protection and Measurements published its most recent report[$35] on "Limitation of Exposure to Ionizing Radiation" in 1993, and this report provides tables that cover exposures to particular organs.
The NCRP has commented on security scans: "NCRP has recommended that the cumulative effective dose to an individual member of the public from such x-ray systems used in security screening of humans should not exceed a control level of 0.25 mSv y–1 at a given venue." [i.e. 0.25 millisieverts per year]
And as the FDA describes in its response, "The recommended limit for annual dose to the skin for the general public is 50,000 µSv. The dose to the skin from one screening would be approximately 0.56 µSv when the effective dose for that same screening would be 0.25 µSv. Therefore the dose to skin for the example screening is at least 89,000 times lower than the annual limit." (my emphasis)
Parenthetically, though I'm not gonna shell out $35 to find out, I'd be interested to know whether the radiation limit for your skin were significantly larger than the limit for your spleen or gall bladder, or whatever. Obviously, the skin is exposed to a great deal of solar radiation, and it grows and falls off. Yeah, you can see how deep my knowledge of biology and medicine is.
#2: The scanners are exposing people to hard [higher energy] x-rays, contradicting the TSA's statement that people are exposed only to 'soft' x-rays. Helical Tryst points out that the x-ray source is a 50 keV X-ray tube, which generates both soft and hard x-rays, and is comparable to a dental x-ray.
Now I haven't exhaustively checked everything the TSA has ever said, but the search TSA button on their website suggests that the phrase 'soft x-ray' appears nowhere on the entire TSA site. There may also be just some confusion about terminology, since backscatter imaging (the technique used by the scanners) to some extent favors lower energy X-rays. As you ramp up the energy, scattering increases, but momentum conservation makes it more likely for the X-ray to be forward scattered.
Anyway, the comparison between dental x-rays and the scanner devices is fair, in terms of the maximum energy of the individual X-ray photons. But the important measure of comparison between these two similar sources is the total dosage. Googling doesn't provide much agreement on the exposure from a dental x-ray, with estimates varying from 1 mrem to 25-35 mrem (though the larger numbers may be for a complete series of x-rays, rather than a single shot). And the exposure from the scanners is limited by the TSA rules to 25 µrem, or 100-1000 times less than the dental x-ray.
So if you're concerned about the TSA pointing an X-ray squirt-gun at you skin, you should be concerned about your dentist pointing an X-ray garden hose at your fucking head. (And you should be. There is no completely safe dose of radiation. There's a reason you can no longer use a fluoroscope to see how well your shoes fit. But the health of your teeth is more important than your shoes.)
#3: "With respect to errors in the safety reports and/or misleading information about them, the statement that one scan is equivalent to 2-3 minutes of your flight is VERY misleading. Most cosmic radiation is composed of high energy particles that passes right through our body, the plane and even most of the earth itself without being absorbed or even detected."
This latter statement is true, but is itself highly misleading. The units we're looking at here are rems (or millirem or microrem), and the rem is itself a peculiar derived unit, the roentgen equivalent man/mammal, which defines the radiation exposure not in terms of the total amount of cosmic whatzits whizzing through you, but in terms of the total energy actually absorbed (rads) by the body, weighted by factors associated with how biologically harmful the particular type of radiation is to mammalian cells. So the fact that cosmic neutrinoes are slicing through you without doing any damage is irrelevant. Measuring the radiation actually absorbed by the body, the scanners are indeed equivalent to a few minutes of air travel.
With respect to the larger issues of safety vs. freedom, I think in the end we should be willing to live with a certain amount of risk. When you get on a plane, you know there's a non-zero chance that the engines will fall off or some other accident will occur that will kill you. (And, of course, every time you get in your car, you're accepting an even greater risk of death.) Terrorism is not so different a risk, and I think we should be willing to live with a certain amount of risk, even if that means that government officials don't get to grope 8-year-olds or probe your cavities. And if groping and/or cavity searches are the only way to really have an effective backscatter x-ray system in place, then we can do without having a backscatter x-ray system in place.
If the terrorists happen to succeed in dropping planes like flies, then maybe we would reconsider the proper balance between safety and freedom.