A Quick Prediction
Y'know, I loves me most of what Geoff Johns writes. But that doesn't mean he isn't sometimes incredibly predictable.
That link is to the first four pages of Superman: Secret Origin #2. And with those four pages and what I know from issue one I already know exactly why -- in this new continuity -- Lex Luthor hates Superboy (and by extension Superman) so much.
Here's what we know: in the first issue young Lex runs out of his father's house and the clearly abusive man yells after him. It is also implied that Lex has a sister (who we never know we won't see at all down the road). In the preview Lex's father nearly slips off a cliff while drunk when his brakes mysteriously fail.
See where I'm going with this? Superboy saves Lex's father's life. And I bet you before that issue is up Lex's father kills his daughter in a drunken rage. If Superboy hadn't saved him from that "accident" then Lex's sister wouldn't have died. And that is going to be the reason why Lex Luthor hates Superboy.