1)In that episode where he stoped the nuke by jumping up and disarming it ..how did he get back down to earth
2)
I think it's simple why he doesn't fly ..it's too expensive.Now it might have gotten cheaper as new techniques have been implemented thus why we have seen Kara fly lately.Before they would have had to use it sparingly between eps and when they did'nt have him fly people would be like ''oh why did'nt he just fly like he did last episode''.
Now if you want to get scientfic why can Superman fly ?What makes him fly ?
Strength comes naturally he just lift's something and relizes he is strong.
Speed again he runs normal next thing he is moving very quickly
invulnerability It's just there he puts his hand in a shedder and nothing happen's
X=Ray vision Suddenly effected him and he had to learn to control it..after having a look in the girls locker room..well done
Heat VisionSuddenly happpened when he got horny and had to learn to controlit
Super hearing Manifested it self when he was blinded
Flying he is going to have to learn it wont just happen.
That all said I would like to see him fly at some point