Yes, a bit of cruelty underlies the laughter—as it should. Remember: the Rapture nuts were running around for months predicting that a tiny handful of them would ascend into heaven on Saturday night because God loves them so much. The rest of us—those whom God hates—would be left behind to watch our non-Raptured family members, friends, neighbors suffer and die for a few months before God finally got around to destroying the planet and everyone left on it.
This is bloodlust masquerading as piety—"So long, suckers! God doesn't love you! Enjoy watching your kids die!"—and it's crueler than any Rapture joke I've heard. Cruel people should be cruelly mocked.