I really like your assessment of the film here. The bolded statements indicate, to me, a level of emotional maturity in your analysis.
People too often expect to see "giant, grand gestures" in film, because to them, these are necessary for the watchers to "feel something" themselves; everyone laughs or cries when something extraordinarily funny or sad happens on film, but the more muted moments of emotion are often overlooked, unless the director makes a conscious effort to make these moments appear grand (e.g. this summer's The Way Way Back, when the water-park manager helps the kid not feel like an outcast). In The Way Way Back, for example, you can tell by the music and the cinematography and the acting that these small gestures leave big impressions on the child.
Now we have two stances we could take: (1) either Snyder didn't effectively portray how deeply these gestures (Pete helping him stand after being bullied, Pete keeping his secret, humans generally looking out for each other) affected Clark, or (2) Clark wasn't affected in some deep life-altering way (like the kid in The Way Way Back) each time he saw some small nice thing occur, and portraying each as some enormous moment in his development would have been melodramatic. My view is the latter. Clark had plenty of reasons to believe in humanity's goodness without having people lift him on their shoulders and celebrate his existence.
Moreover, while the movie didn't show us every moment of Clark's life, he lived in OUR world, meaning he saw all the great and small kindnesses each of us have seen in our lives (the sense of companionship in NYC after 9/11, the unity of the country after the Boston Marathon bombings, simple friendships, kind gestures). We can't ignore that he's part of our world, that he grew up here--if we were to take that stance, we'd have to take a similar stance on all characters in film and literature. And, simply put, such a stance would be exhausting, because we'd need to see each character's painstaking development from birth to now, in order to answer "why doesn't he hate the world?"
In addition, Jonathan clearly does his best to explain to Clark why people fear him: "People are afraid of what they don't understand" (or something like that). So Clark, while he finds it difficult, doesn't go berserk and rip off the bullies heads... because he's a strange, misunderstood kid (running into closets after seeing through his teacher, saving buses of schoolchildren), and he has been given the tools (from Jonathan) to understand why the bullies might target him.
Finally, the film repeatedly states the limitations of humanity: "...but in time, they will join you in the sun..." So it's not like Clark worships them. He knows that people make mistakes. He knows we're all human.