Symbolism, Imagery, Allegory
We know; we know. A crucifix—an image of Jesus Christ on the cross—is a symbol of Christianity. But in The 5th Wave, when everything (including organized religion) has gone haywire, it's more layered than just a testament of faith.
Here's what we mean:
At the beginning of the book, Cassie comes across a wounded soldier during one of her supply runs. It hadn't been that long since she'd watched one of the Others (disguised as a human in military gear) murder her father.
She's nervous, and doesn't know how to establish trust. When she asks him to raise his hands,
[…] the stunted light kissed his bloody hand and flicked along the length of something long and thin and metallic. (4.41)
Cassie, taking it for a gun, shoots him dead.
It wasn't a gun, though. "It was a crucifix" (4.45). Whoops.
Looking back on this murder—which she does often, because her conscience is plaguing her—Cassie thinks the soldier wanted "to die with a sliver of his humanity intact" (4.38). Maybe so. But for Cassie, the cross symbolizes something else. She blew away a guy clutching a crucifix with an M16, an action that symbolizes her loss of faith—not of her faith in god, but in her ability to trust other humans.
Cassie never quite regains that faith, at least in its original form. When she finally learns to trust again, the person she puts her faith in is Evan, who's an alien. (The Crucifix Soldier is probably rolling in his shallow grave.) She's set aside her questions about faith and on to the urgent task of figuring out why so many aliens want her and her fellow humans dead.