Snake was always his own man, even if he was being used by the government and screwed over (which happens to a lot of soldiers). The character always fought for what was he believed right and to make the world a better place. I also think he's more grounded and consistent in his convictions than Big Boss, who later descended into villany to combat Cipher, and make a profit on war. Snake may have gotten more tired and depressed in MGS 4, but he never changed who he was. It's a consistency that I appreciate.
Also, remember when Snake joined Philanthropy? That was to stop the proliferation of Metal Gears around the globe after Ocelot had leaked the design specs for REX, after Shadow Moses. He felt it was his moral obligation to put an end to Big Boss' legacy. He also wasn't looking for glory or recognition, and that, to me, is the mark of a well-written hero.