Even with McVeigh, these can be dealt with using typical policing methods. Even though some think McVeigh didn't act alone, there is no elaborate network that is crouching, waiting to commit another OKC. The militia movement is barely existing and there are no reports of militia-types celebrating over the 9/11 attacks.
The militant Islamic threat is different. It is supported by large groups of people, both overseas and the US, to varying degrees. It cannot be stopped by typical police methods. In fact, I don't think it will end with military action either, but significant inroads can be made to reducing the threat.
Great point.