On second reading, I noticed that the natural gas vehicles you were most likely referring to were the 800+ highlighted in your original post?
It was my understanding that for vehicles to qualify, their mpg's had to be a certain amount worse than the vehicle they were being traded in for, so while there are obviously exceptions to every rule, the emissions technology on those older natural gas vehicles still must not have compared well enough to the emissions technology on the newer vehicles.
While money was obviously a big factor in the program (boosting the economy, helping the automotive industry, etc.), wasn't the overall intention for creating the program a means of helping to clean up the environment? As crazy as it sounds for a person to say it in this day and age, money ain't everything.