Is it so hard to believe that Jonathan Kent just wanted to protect his son from what would happen if the world found out ? Look what's happening now in BvS, he's hated by half the world even if he's loved by the other, and in trial for saving Metropolis and the whole Earth. That's actually pretty mild compared to what could have happened ! The gouvernement could have turned 100% against him and try to take him down, which would have ended badly for them probably, but equally as bad for Clark who would have become an enemy of the state. I believe that's what Jonathan feared, and why he made seemingly stupid decisions. He's not perfect and that makes him human. Same goes for Ma Kent and her lines in the BvS trailer, you can see she's talking to her son she loves and raised all these years, not to this super being everybody else sees. She wants what's best for him. Like every caring parents I would say...