"What is real? How do you define real? If you're talking about what you can feel, what you can smell, what you can taste and see, then real is simply electrical signals interpreted by your brain."
The aspect you inquire about is not the most disenchanting aspect of the movie to me. The part that I have a hard time suspending disbelief about is the premise that Zion is an underground city "Deep underground, near the earth's core where it's still warm." So all humans not plugged into the matrix live in deep caves warmed by the still warm core in an otherwise cold earth ... not likely.
Maybe the Neb really is a 'honeypot' as you put it.
Nevertheless, I will be standing in line on May 18th. I have waited years for this ...
That would be where the "Hollow Earth" theory comes in. . .