There are some nasty people in The House of the Scorpion. We're thinking of El Patrón, of course, but also of Tom, the Keepers, and plenty of others, too. None of these people are very nice to Matt, and he could just as easily be just as cruel. But he's not, and that's because Matt is a compassionate, forgiving guy. He's got humanity in spades. Although he struggles with his own identity as a clone, we're never in doubt of Matt's humanity. No matter what anyone says, we know that Matt has a soul, and that it's a good one. And we know this because he struggles to be compassionate and forgiving at various points throughout the novel. He struggles, but he succeeds. He feels for El Patrón, for example, but he's still strong enough to walk away from him and forge his own life. In the end, Matt's ability to be compassionate and forgiving set him apart from El Patrón, and will make him a much better ruler of Opium.
Compassion isn't easy for Matt, who is surrounded by jerks most of his life, but he learns the value of living without anger and hate as he grows older and decides to avoid the dark side (unlike Anakin Skywalker).
María, more than any other character, represents the book's theme of compassion and forgiveness.