I suppose the trap could've been in Boone's head, just like his sister and the monster.
I think it's possible the monster is real but that it's also showing up in people's heads. So the 'real' monster killed the pilot. But in Boone's crazy dream, it kills his sister and he's actually relieved. We don't know what happened when Locke (probably) imagined seeing it but I figure he lived out his dream of fighting it and winning (being the outdoors guy who can do anything). So the island causes fantasies that may or may not include the monster, but there is a real monster that really did kill the pilot and smash some trees down in the first couple episodes.
As much as I like the show, I worry that they won't be able to explain everything they've laid out in the first 13 episodes.