These tunnels are connected/same as the area where Ben was judged. Ben and Locke went under the temple and Ben proceeded to fall even further below - this suggests the two locations are analogous/connected via the tunnels.
The tunnels may explain how Richard was able to bypass the sonar fence on visiting the Dharma Initiative. He states that the fence may keep other things out but not the Hostiles.
Richard's inability to die may also be the reason he was able to get through the sonar fence.
Similarly on abandoning the Barracks in S3, Sayid makes a comment that they left as if thirty people vanished into thin air - possibly a hint at the existence of the tunnels.
The Blast Door Map makes similar note of underground conduits or tunnels.
The tunnels and the Temple were left buried underground after the volcanic eruption. The Temple walls, as seen by Jin and Rousseau, are partly visible, as its walls would naturally be taller than the actual Temple. The tunnels are probably old buildings and weren't intended for their present use.
The main entrance to the tunnels is the one accessed inside what will be Ben's house back in the Barracks. It's the area he went in to summon the Smoke Monster against Keamy. DHARMA built their Barracks over it, forcing the Hostiles to have to swim underwater to get in to the tunnels. Once Ben and the Hostiles purged DHARMA, they reclaimed access to that entrance.
The access door in Ben's closet is an ancient stone door that is clearly above ground. The DHARMA initiative would have had to have seen it in their construction and would have been able to access it regularly. The reason they go through the waterfall to get to the tunnels, is because it was the closest entrance to where they were at on the Island. The tunnels span all over the Island, and there are many entrances.
DHARMA knows about and has entered the tunnels since they built a modern access to the stone door behind the "leader's" house.
DHARMA is fully aware of the entrance to the tunnels from the house Ben ends up occupying and use it to control the smoke monster.
The Others off-Island interests (Paik Industries/Widmore Industries) won the contract to build Dharmaville. They purposefully connected the tunnels to the door in Horace's house, but did so privately, never telling Horace and DI about them.
The Others manage to get around the Island so quickly and silently due to use of the tunnels.