I think the fault here lies in the flashback scenes that were chosen. There is nothing really in the movie to suggest that at other points in his life, Jonathan did not be the type of father figure your are suggesting. In fact, dialogue in the movie specifically states that he had been, even if we don't see it.
But that's part and parcel of the film's core problem. Everything that's important to the mythology and spirit of Superman in this film is just paid lip service to -- there's dialogue referring to it, but it isn't shown, isn't earned, and what we are shown tends to work against the ideas and ideals hinted at in the dialogue. That's deeply flawed storytelling, failing to live up to one of the most basic rules: show, don't tell. Whatever worthwhile ideas this movie had were hampered by a very problematical execution.
The scenes that we are shown in the movie specifically relate to the times in Clark's life when his parents were worried that his secret would be revealed--and there is no arguing that Clark would be taken away from the Kents if it were.
Oh, I can argue with that. They might try to take him away, but really, how could they hold him? Not to mention that, despite the popularity of the trope of the government taking people away, all it would take is some publicity and there'd be a public outrage over such unlawful detention of a minor, and legal action could be taken to stop it. It would be a PR disaster for the government to claim that this innocent-looking boy was a threat that needed to be locked away and experimented on.
Really, that's part of why I hate the fictional trope of keeping special abilities secret. Secrecy just encourages abuse and injustice. Really, if you had superhuman abilities and were on the run from the government because of it, the absolute best thing you could do would be to hire a lawyer, call a press conference, and tell the world everything. Our legal system and free press, when they're working right, are the greatest tools against injustice and persecution ever devised by humanity.