The line was dumb
When Clark ask "What was I supposed to do? Just let them die?"
Pa Kent shouldn't have said "Maybe", but instead "Of course not, but you have to be careful and make sure you aren't seen."
In the end, Pa Kent was arguing that his son's secret was more important than a bus full of soon to be dead kids. Of course he can have that opinion, but that isn't something he can say out loud without him coming off as selfish as hell.
Pa Kent was position on Clark using his powers was "he doesn't know". He wants to protect his son, but at the same he knows his son possesses incredible powers. His first inclination was to keep Clark's alien nature and abilities a secret. Rather than motivate his Clark to put on a brightly colored costume and go help people. If the conversation Clark and Jonathan had was in an X-Men movie, nobody would question or debate it. Because we know what happens to people who are different or have "freakish" powers, when they're exposed to the general public.
A big theme in MOS is trust and faith. In the tornado scene, Clark was ready to jump into action, but his father was willing to make the sacrifice to keep Clark's secret. Because the world wasn't ready to see what he could do. Clark trusted his dad's judgement and by extension, put faith in his decision. Since they were just having that conversation in the car. However, Clark kept helping people long after his dad died and before he was given the suit. When he finally made his debut, it was at the beginning of a world wide crisis. He trusted humanity and with convincing (the Smallville fight), the military at least, began to trust in him.
While the death of a parent in comic IPs is always tragic (Meredith Quill, Jack Murdock, Ben Parker, Thomas and Martha Wayne, Howard and Maria Stark), someone made this gif set of Clark's decision to not rescue his dad and Barry's decision to not save his mom.
http://dailydcheroes.tumblr.com/post/158415818418/man-of-steel-2013-the-flash-2014
It really draws into focus what the people of MOS were trying to accomplish. Clark is defined by his decisions and the trust he puts in other people (Ghost Jor, Jonathan, Martha, Lois, Bruce, General Swanwick), while Barry is defined by his tragedy and makes his decisions to try to change the outcomes in his favor (Nora dying, Henry dying, Iris dying, Flashpoint, etc). Barry ultimately ends up learning the same lesson over and over, while Supes wrestles with the things he can't change (death all around him and the world constantly needing rescuing).
With great power, comes great responsibility. Supes does the best he can, but that's not always good enough.