I think the main reason that is, is not because they're trying to brainwash the public into thinking that humans are absolutely good, but it's there cause it is easier to understand and relate with. In reality, good and evil is very blurred, it really depends on what side you're on. Most people would consider ISIS evil, but people in ISIS believe they are doing some good, I believe they're evil but it's just pointing out how the notion of "evil" and "good" is not objectively universal. However, this concept has two problems in a movie industry.
1. It's complex
2. It's not satisfying.
A common thing in movies is that they try to appeal to the lowest common denominator, they want the movie to be easily understood and satisfying to as many people as possible (as they can make more money this way). So a complex moral framework isn't gonna be very great for your summer blockbusters or casual games like Kid Icarus. But that's fine in a way, these movies and games aren't designed to make you think about philosophy and morality, they're designed to be an entertaining ride, which is probably why most people love it, is because they see it as an entertaining ride, rather than a real statement on humanity and society. So I would wager the reason people love Kid Icarus is not because they agree with the sentiment that humans are absolute good, but it's more that they haven't even really considered it, they enjoyed the characters, the story and the ride of the game, they didn't really take note of any message behind it or at least didn't get the same message as you did.
The other thing is of course, a grey moral framework, while interesting, is not satisfying. Almost every game, movie or media device will have a protagonist and an antagonist. Someone who is inherently good and someone who is inherently evil. The person who is inherently good is usually a human, because people can relate to them. "He's a human, I'm a human, I can relate to him!", it's going to be harder to relate to an alien species, which is why movies like Avatar and District 9 spend a good portion of the movie trying to relate to the audience that the alien species are the good guys,. If the good guy was Jake Sully there'd be no problem, he's a human and you can relate to him, it's not about humans being absolutely good, it's more that we are humans and we generally support our own kin. Regardless, if we had no real good guy and no real bad guy, a lot of the time it can leave an audience confused and not so happy. Some shows have done a terrific job of making a moral grey framework, like Dawn of the Planet of the Apes and Game of Thrones, which try to enforce the idea that "we're not saying who is good or evil, we're just letting you decide for yourself".
So yeah.