Like others have said, I never actually felt sorry for the cube because there was no reason to do so.
The cube itself is a soulless hunk of plastic no different than any other cube found in the game aside from having some hearts scrawled on it. Had you simply gone through the level without Glados saying a word, nobody would hesitate to dispose of the cube. The cube was not some unique creature that you destroyed. It was an easily replicated object, as shown by it's presence in the last screen in the game.
However, Glados constantly tries to suggest that there is some kind of bond between you and the cube. She thinks that the player will immediately attach them self to lifeless cube, just because she says that they should. It shows her limited understanding of how humans really work, leading to her surprise when players don't hesitate to lob the cube into the firey pit. Just because she says you should feel attached to the cube doesn't mean you will. There has to be a reason for you to like a character. No story can expect you to like a character just because you are told to do so. This is why I always enjoyed the humor behind the companion cube. Not only is it a funny part of the game, but I also see it as a mockery of poor story telling.
Of course a lot of player apparently became attached to the cube so I'm not sure what to think of that. All I know is that whatever humor I originally associated with the cube is now long gone after every joke about it was driven into the ground.