Could be that the guy is an anti-christ figure who doubts the plausibility in believing what you cannot see. So he steals the angels egg from the girl/believer and smashes it to confirm that there is nothing inside. Then the world floods which could be God's angry response to a non-believer destroying the potential for life. Though you can hardly blame him - the world is in ruin, no one knows who they are, it's been raining for six weeks, lots of reasons to not believe the existence of a god.
But in the scene prior he does confirm that the dove that left Noah's ark did exist (found its fossil), which would prove the tale of Noah's ark and christianity to some extent. Soon after when he smashes the egg...with a crucifix he'd been carrying the entire movie...the girl is forced to come out of hiding and is sacrificed to produce new eggs that are perched upon stalks pointing to the sky, and you can see life inside of them unlike the false egg the girl was hiding from public view. So in this sense the girl is an antagonist who is preventing the salvation of earth and the guy directly helps to bring life and light to a dystopia and is rewarded by God for showing his faith. This the interpretation of the film I most agree with but you could easily argue the exact opposite and it would completely change the meaning of everything.