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Card does not definitively say whether he believes that human nature is inherently good or evil. All people are complex creatures filled with conflicting desires and attributes. As a result, there is no such thing as pure good or pure evil. Earlier on it appears that Ender represents pure good and that Peter is pure evil, but these distinctions quickly fall apart. Ender certainly tries to be good, and he cares deeply about others, but the summation of his attempts to be good could hardly be called so by the end of the novel. Ender kills Stilson and Bonzo, as well as the entire bugger race except for one queen. Peter, on the other hand, is motivated by nothing except personal gain, and he does not care for people at all. Yet Peter saves many lives by coming to power the way he does. Even when we act for good reasons we cannot be assured of a good outcome. On the other hand, if we believe that certain ends are good, like Graff and Rackham, we may commit evil acts in order to achieve them. However, what matters in the end is the result as much as the person. Peter may have done some good in his life, but it was unintentional, and if he made no attempt to right the wrongs he committed. Ender, who never wanted to hurt anyone, feels responsible for many evils, and he dedicates the remainder of his life to remedying those that he can. A love for humanity and the desire to do no harm to our fellow human beings is a good trait, and even if it leads to certain bad actions or outcomes, those who have it will always try to do the right thing.
Everyone seems to be manipulating everyone else in this book, suggesting that manipulation is a universal human trait. Valentine says as much to Ender in the end of the book. At that point he feels as if his entire life he has been manipulated. Valentine points out, quite rightly, that we can never free ourselves from the influences of others, and that people will always be manipulating others. However, what we can do is decide who we will let influence us. She is appealing to Ender to follow the path that she has set up for them, and he agrees to go, for reasons that differ from hers. Ender wants to go to try to help repay his debt to the buggers. This fits fine with what Valentine said, since he is able to follow the course that she wants him to take but for reasons that make it a valid option for him. The choices we make in life are often dictated to us by others, but what Card seems to be suggesting is that we will be happy if we can find our freedom within the road that somebody puts forward—that is, you can trust the influence of those who care about you.