Sometimes a giant toad is just a giant toad…and sometimes it's a metaphor for socio-economic inequality.
You may have noticed that the scene right after Ofelia's battle with the giant toad—you know, the toad that grown monstrously large from feeding on nasty grubs—is the dinner scene, featuring Vidal, the priest, and other important people. These bigwigs are gobbling away at all their fancy food, while the rest of the families are being rationed do to the war (or post-war) conditions.
In the same way that the toad is syphoning the life of the fig tree, the Spanish upper class is killing the lower class by hoarding Spain's limited resources.
But sometimes a giant toad is just a giant toad…and sometimes it's a metaphor for pregnancy. (Yikes.)
The toad could also be representative of Ofelia's baby brother. Go back and check out the shape of that tree again. It looks a lot like the uterus and fallopian tubes. And the tree—like Ofelia's mother—is slowly being killed by the being that lives inside it.
And in case that wasn't morbid enough for you: think of the toad's death. As it dies, it regurgitates a large sack. This imagery is reminiscent of afterbirth, when the placenta (also a large sack) comes out of the birth canal.
We know; it's super-visceral. But hey: welcome to the wild world of Guillermo del Toro films.