As a general rule, I consider the music playing over the main title to be the main theme. In this case, that's "What Are You Gonna Do...", and the variation of that theme is playing when he walks out of the fortress and prepares to take flight for the first time as a voice-over from his father describes what he could be to the people of Earth (part 1 of "Flight"). That totally makes it the main "Superman" theme to me. I don't determine a main theme by whatever's played most (if I did, the Zod-centric action music would probably take that title here) - it's not how often it was played that matters, but in what context, imo. Contextually, "What Are You Gonna Do..." announces itself as Superman's theme to me.