The choice depends.
Superman Returns was technically the better movie (by far, in fact). Superman Returns had the better script. Man of Steel had the better actors, but Superman Returns utilized its cast a hell of a lot better. Which movie is more faithful to Superman's character and mythos? Neither and both.
But personally I liked Man of Steel a lot better for one reason and one reason alone: when I walked out of the theater, I was excited to see where it'll go from there. With Returns I really had no real desire to see what's next. It wasn't because I disliked the film (that came with subsequent viewings, I liked it quite a bit the first time I saw it), but simply because there was nothing in its set-up that would interest me to see expanded and/or explored.
For all its many, tremendous faults, Man of Steel at least has some place to to go. It may be a better place, it may be a worse one, but it's somewhere!
When Superman finally came forward to the world it didn’t matter that they would fear him, because in the end he was their only hope, so Jonathan’s fear didn’t even matter in the end for the plot.
Not that I'm crazy about Jon's portrayal in MoS myself, but his fear was pretty well-established out in the movie. The humans didn't end up fearing Superman, because they were being pummeled into the ground by an army of Kryptonians and he was literally the only weapon they had to defend themselves-- and even then, they didn't really side with him until the half-way mark. Up to the end of the Smallville battle, Superman was fighting alone.
Jonathan's point was Clark should hide until humanity would be ready to see how necessary he is and welcome him, which happened with the alien invasion. A little on the nose, I admit and... well, let's not mince words, pretty damn terrible writing all around, but the point was made. It was just a pretty ****** point to be made.