First (and most importantly), I see no reason to assume that there's something special about Earth, per se. The prime universe is what's special. Since Owlman is conducting his search for the prime universe from Earth, Earth-Prime is what he'll find. If he was on Krypton or Oa, he'd find the prime version of that planet.
Second, Owlman is a genius, explaining his plan to Superwoman, who may be smart, but doesn't approach his level of intelligence.
It seems reasonable to assume (especially when explaining things to a narcissistic psychopath) that a truly smart individual would dumb things down enough for her to follow.
Finally, it's not entirely clear what his plan is, specifically. Will the QED destroy the Earth - or the universe? Would blowing up Earth-Prime destroy all Earth's - or literally destroy the entire multiverse? Owlman may want to remove Earth from all the universes, or actually destroy all reality (including himself, presumably).
Owlman refers to man as a cancer he's cutting out; man, not life in general. Killing someone and cremating the body doesn't seem much like "cutting out a cancer"; that tends to imply the patient has some chance to live after the operation. This could, in fact, mean that he's destroying all Earths rather than the entire multiverse. Certainly, the explosion we see just appears to take out one planet, not that entire reality. (That said, we of course don't know what the impact would have been if the explosion did happen in the prime universe; and our earlier caveat about Owlman and his audience can probably cover a certain degree of imprecision in the description).