Common theory is that the amusement park is a curse LeChuck have put on Guybrush, and that it isn't real. But I have a theory that it's the amusement park world that's real, and that there's some magic in the real world that takes the two boys to the world of Monkey Island. Maybe a portal to a parallel dimention or something. Chuckie finds Big Whoop which gives him powers that still remains with him when the boys return to our world, which explains the glowing eyes. Or something. I like the idea of two boys just playing, but I just think there's a little more to it than that.
Or maybe LeChuck just put a curse on Guybrush in the end of the game to get out of a difficult situation.