It makes more sense if you look at it this way: they aren’t doing this to keep out terrorists. They are doing this to “protect” americans from dangerous foreign ideas. Things like gay marriage, multiculturalism, universal healthcare, world court and international agreements, tolerance for different cultures.
Remember the people carrying this out are paranoid, that is what they do. But the people ultimately behind this are the religious right and the neo-cons of the republican right. The same people that want to “protect” Americans from things like learning about evolution in school, Al-Jazeera on cable, and off colour lyrics in songs.
The people in charge of “homeland security” down south know exactly what they are doing. They are trying to keep Americans sheltered and ignorant and acquiescent. Sadly, I suspect they even think that is what is best for the average American.