I think most people in the Bay Universe would try to forget about the Transformers entirely and wouldn't want to really question their sudden disappearance.
The gap between DOTM and AOE is the only time I've actually wanted some kind of comic or other media to fill in the details of what happened inbetween movies, and they never bothered making any.
What do you mean "think happened"? That's, like, exactly what did happen... as the movie itself more or less directly told us. I'm confused by this thread...
But didn't Attinger say that the CIA thought that Attinger's Cemetary Wind were hunting Decepticons? Also I don't understand why didn't Ratchet continued to drive instead of Transforming?
If you watch closely you'll see that the entirety of Cybertron which had been transported to Earth via the Space Bridge collapsed in upon itself and and got sucked back through from whence it came after the Control Pillar was finally destroyed.