Oink. Oink. [That's the sound that a suitcase-shaped pork barrel makes as it passes through the scanner.] This is all about whose lawmakers make short lines a priority and let TSA know it. Being on the "right" side of the aisle probably helps a bit, too. EVERYTHING that the feds do for civilians is affected by pork priorities, and TSA is certainly not immune.
As to small airports, no one is saying that they don't need adequate security; but many of them have ended up with way more screeners than they could possibly need at any season, while busy airports are stretched too thin. I'm betting that the turnover problem is not as severe at small airports, either; with less traffic and shorter hours, the work is not as unpleasant.
(FWIW: It really wouldn't have mattered if the 9/11 hijackers had cleared security at Logan or JFK, they still probably would not have been stopped. They were carrying perfectly [then] legal boxcutters and ID in their own names. I think that they chose to go through the smaller airports in places where they did not live because they believed that *if* the authorities had gotten wind of the plot, they would have been more likely to concentrate their interdiction efforts at the larger airports, distributing photos, etc.)