The author talks about the terrorist/militant/activist groups already inside the US, as part of a look at why fingerprinting at the border, and generally being so concerned purely about outside threats, may not be helping us much. The insider groups come in lots of flavors: anti-abortion, anti-tax, anti-government, anti-jew, ... He wonders if we're squeamish of talking about these groups because of their links to religions we generally agree with: if it's islamic militant groups perverting (and breaking the rules of) their own religion, it's okay: if people come to associate the activities with Islam, that's okay. But if we're stupid enough to associate our own militants with, say, Christianity, people are going to be offended. Maybe it's just better not to talk about it?
We've got terrorists, they've got terrorists, lots of people are unhappy, lots of people are potential victims, lots of people are just bystanders. There's a big picture here somewhere.