I don't think it's even a tunnel- you could see that it was all really old stone on the inside-- i think that it was part of an infrastructure that was there even before the Initiative. It obviously has the power to control the monster, which I assume has been on the island for a very long time. I would be willing to bet there are other places where the new Dharma stuff interacts with the ancient structures already in place. Take the giant statue Sayid and Sun and Jin (spelling?) see when they are on the boat-- it was only feet (with four toes) and was knocked down. Neither the Dharma Initiative or the Others would have reason to build such a thing, so there were most likely people there even before then. The hostiles perhaps?