I've seen 2 spares knocked from below an Xterra actually.
The reason I put mine on top is because it is potentially at risk of being cut or having the bead popped by a rock or the like while under there. Yeah, it's a slim chance, but it's still a chance. Also, those with 33s or larger and no rear carrier have no choice but to put it up there or in the cargo area.

Brent