Cyclops motives for the past couple of years have been mainly to ensure the survival of the mutant species. I always thought this a bit strange because in my mind there is no difference between mutants and humans with powers. So what if loads of people lost their powers? They didn't die because of it.
I'm sure if the Avengers lost their powers Captain America wouldn't move everyone to an island and try and create a separate nation etc.
Maybe its Xavier's fault: he should've taught Cyclops (and the others) to think of himself as human instead of a part of a separate species. Maybe the peaceful coexistence between humans and mutants would firstly need the x-men to not draw a line between the two.