They say they are saving the planet by blowing up a bunch of "Mako Reactors". Because the Mako reactors siphon off the life energy from the planet, they feel justified. The group is a bunch of terrorists but the main gameing population supports them because they play from the perspective of one of the group rather than one of the government.
From our perspective as americans we see things from the other direction, thus we hit the point of saying that the people who do this sort of thing are ultimatly wrong. I think that were we invaded by another country, I don't think we'd worry too much about what was a military target and what was a civilian target because we'd have incomplete intelligence, limited supplies, minimal personell, and we'd have to do this in secret. othewise we'd be sent to a prison. I'm not saying we'd target the civies specifically, but because we were dealing with an invader on our soil we'd target those PERCIEVED as "aiding and abbeting" the foreign power. Or the real Zelous among the "resistance" target anyone whos not fighing...
Ultimatly we'd hit whatever we could when we could if only to keep ourselves in the spotlight.