On the basis of what? NO ONE in the book knows the full extent of Manhattan's powers. Even Dr. Milton goes on to say that "the safety of the whole world rests in the hands of a being far beyond what we understand to be human." And he also says that the extent of Manhattan's powers have only been theoretically tested. Not proven. And with that, Manhattan could learn to how become more powerful, much like Moore did with Swamp Thing. At first he was just a plant monster, until he finds out later that he can be so much more and that the extent of his powers know no bounds.
People have seen what he can do. But again, no one knows for a fact, how powerful he really is. And that's the point of the ending. NO ONE KNOWS. Whether or not Manhattan knows how powerful he is is irrelevant because the people, the citizens of the world, don't have a clue. They see he can do this or that, but they wonder what else he can do. They have to. It's human nature. And in the back of their minds, i'm sure they think "What he goes rogue?" So when big blue blasts of energy blow up all their loved ones, people are gonna "Crap, he's turned on us!"