Couple of thoughts about what it may be (I do not believe it is an entrance to a temple/dungeon):
1. Entrance to a cave that contains a special item (may be a part of a sidequest)
2. Entrance to a Fairy Fountain
3. A tunnel/shortcut to another area of the overworld (connection between areas...possibly the forest/sky temple area and Eldin volcano). If this is a case then you would probably not be able to access or use the tunnel until you completed the Sky Temple and achieved something on the Eldin volcano side of the dungeon that made it accessible (like get a certain type of bomb in the volcano area and blow up rocks that are blocking the tunnel on that side).