Superman has lost his trunks for one reason only IMO.
Realism.
People are obsessed with it. Our superhero films and stories are now full of it.
And because of this obsession with having every single thing about a superhero story be logical, realistic, and representing the time period they are set in recognisably, the people making this film have decided that Superman wearing trunks won't work.
They've mulled it over and come to the conclusion that if Superman were to actually exist in our world, if a boy with powers grew up and decided to put on a costume and save people, he'd wear something that no one could consider uncool.
They've decided that because they can see no specific logical reason for him to wear trunks, especially with this new material which i'm sure doesn't cling to his package like a ballet dancer, that they can't justify using them. Because they would have no way of 'explaining' them.
Captain America went from this:
To this:
Look at everything they've changed on that suit, all for the sake of realism. The helmet, the complete lack of the red and white stripes (other than two red buckles).
I really don't see how we can complain too much about finally loosing the battle for Superman's trunks (for which I very much was on the side of the trunks).
When this 'realism' fad is over, i'm sure they will come back.
Right now i'm just glad the new suit is none of the following:
1. Armour
2. CGI
3. T-shirt and Jeans with a cape
4. Black