JI - I just got back from a trip today, and I've got to say this...yes, the random security checks are bullsh*t. I flew Delta (very good experience), but I did notice that it was the boarding card reader and NOT any human who flashed "random check" for passengers to be screened. Yes indeedy do, a prolific terrorist can certainly make a deadly weapon out of a pacifier, but if he's really clever, he'll hang back and count out how many passengers make it before the "random" one is selected, then get in line and pass right on thru. IT'S A JOKE.
Well, I certainly can't speak for all airlines, but I know from first-hand experience that many travelers are already pre-selected long before they check-in and that there is nothing random about it. The TSA considers hundreds of factors (of which we gate agents have only figured out a mere 10 or so) which will ensure you are selected for additional security. Destination information, one-way vs. r/t travel, name (compared to black lists) are just but a few which will trigger a 'selectee' status. (I've also noticed many people who change their itenerary at the last moment, such as flying revenue standby for an earlier departure,) will trigger a selectee status.
As for counting passengers in line, I have personally had 7-8 selectees all board in a row and all of them get pulled aside; a gate agent also has the authority to make someone a selectee based on actions of the customer/passenger, or if there are simply not enough people being searched at the time. So it's a combination of random selections, human intuition, and TSA's selection process which determine if your checked luggage is submitted to CTX scans and your person and carry-on baggage is subject to additional screening.
It's not nearly as simple as picking every third person in line.
In addition, no person may be 'cleared' from 'selectee' status for any reason, with rare exceptions. Law enforcement officers, 2-year olds or other small children are not in any way exempt from additional security screening if they are selected. The only exceptions to my knowledge are FBI, CIA, NSA, US Marshalls, or any member of the military on active duty with written orders in hand. In order to be removed from the list, I actually have to call a GSC to clear the entry. (It cannot be processed locally.)
But this is just my insight from behind the ticket counters and gates of Minneapolis-Saint Paul International...