I don't think they handled the trust subplot all that well. They did show clearly that Superman was willing to act benevolently toward humans, but the way the humans responded after he brought down that surveillance drone made it seem as if all was good since it was such a light, easy-going scene. But really, at that point Superman should just be beginning to earn trust, and future films would need to better explore it. I thought a more appropriate response from the humans still should have been extreme caution and skepticism, considering they just have to take his word for it, and one series of actions helping to defeat Zod's force. But I guess they were trying to end the movie on a light note across the board.
I don't think this Superman was too flawed for the character. He's learning his way as a superhero, but already he seemed to have a pretty clear moral compass. Of course, he's not going to be the idealistic silver aged Superman/Moore's Supreme. Film studios don't have enough faith in the audience to go with something that "revolutionary" in the modern age of film. So considering that, showing more flaws than, say, Reeve Superman is inevitable. They touched on this in the Superman and Justice League animated series' as well. It's part of the paradigm. An absolutely self-assured Superman would simply not work in any remotely "realistic" world that WB is trying to put together for their Justice League. You have to treat the whole universe as being different and more simplistic for that to work IMO. Otherwise Superman would just come off as naive.
By the way, was a good explanation given for why Jor-El merged that genetic coding into his son, apart from creating a plot device for Zod to want to seek him out for reasons other than revenge? I thought Jor-El thought the "old Krypton" needed to die? And it seems like he didn't explain to Kal-El that he did it or why he did it. So. . .what was he trying to do? He went to a lot of effort and took a lot of risks to do it. Seems like allowing Zod to have it would have been a better option if he really wanted to allow Krypton to continue on in some capacity. He may have wanted to be a dictator, but dictatorships come and go. The core of their society was not replaceable. . .but again, I thought Jor-El thought it needed to die, so. . . I just didn't understand what was going on there.