I think a huge point is being missed here, which is objectivity.

The Brotherhood see their actions as overthrowing a corrupt government that fails to care for its citizenry. It believes it can do better. Shin and Storm believe that.

That doesn't mean everyone else sees it the same way. There will be opponents, there will be opportunities for heroes and villians to be made here. I am not expecting (and don't want) everyone to back the Brotherhood. I am not expecting everyone to go against them either.

You make up your own mind and then side accordingly.

I am trying to create something that involves people on an emotional level and allows them to participate in fighting for a cause.