Lex knowing Superman's identity, along with President Lex, were two HUGE balls that DC dropped. There was unlimited potential in both ideas, which could (and were) easily be linked.
But no, rather than making it a huge deal, Lex was basically the same behind-the-scenes player as usual, not making any fuss and then suddenly went crazy, hopped up on radioactive Venom and climbed into his green and purple powersuit. You can thank Jeph Loeb for that last nonsensical part.
What's worse is the potential was there from the beginning. Lex threatening Batman with all his governmental power, talk of (ironically) registration or some kind of Justice League agreement, etc. But, ironically like a presidental promise, none of that potential came to pass.