It would certainly seem that's what I'm supposed to think.
What concerns me more than whether or not people are inside it is what exactly it is. At first I thought it was another plane or sub or something that had been buried. Now I'm wondering if the hatch is a part of the island itself. Maybe the island is really a big government facility, and the sand, beaches and forests are its coverup. Area 51 in paradise.
Or maybe it's sort of a bigger version of Noah's ark, only made in anticipation of the nuclear wars, rather than a flood. Could explain the polar bear in the first episode.
