Did you find the room full of poems dedicated to the companion cube? I think it's more the reaction that previous test subjects had to the cube combined with the desire to disobey GLaDOS when she repeatedly says that the cube cannot speak or help you. But if you wait long enough to kill it, she says "If the companion cube could speak, it would say 'Go ahead, go on without me.'" It's mostly the fact that the fact that it is reinforced several times that it is just a cube, so much so that it almost seems that GLaDOS believes that you will see it as more, and you wonder if you should.
That's just a theory, the fact that it appears again at the end helps (is that a spoiler? the game's been out a while now and it's not as though anyone answering this question will not have played this game right?).