Because Green Peace doesn't have branches calling themselves Green Peace and advocating racism or secession/overthrow from/of the gov't.
Militias that do good need to advertise better. If any of their membership are advocting the teabagging and birther nonsense, they're going to get a bad rep.
Here's a little something of interest for you:
FBI Whistleblower: White Supremacists Are Major Domestic Terrorist Threat
....... Mike German worked for the agency for more than 15 years and quit last year. On June 5th, he wrote an editorial in the Washington Post advocating that law enforcement pay more attention to organizations that produce so-called lone wolf extremists like Timothy McVeigh who was executed for the 1995 Oklahoma City bombing and Eric Rudolph who planted bombs at the Atlanta Olympics, abortion clinics and a gay nightclub. German writes that “lone extremists pose a challenge for law enforcement because they are difficult to predict. It’s like searching every haystack for a needle. Perhaps we’d have better luck if we paid more attention to the needle factories.”
http://www.democracynow.org/2005/6/13/fbi_whistleblower_white_supremacists_are_major