In the movie, it mentioned something about wanting the autobots' ship to be under human control until in was off planet//left earth. (Not that a human shuttle could have controlled an alien ship if the autobots didn't want it to. I think it was a gesture of good faith on autobots' part.)
That was a great emotional scene ::even though I knew there was no way they'd kill them all off in one sweep like that::. Loved the score.