From Zelda Wiki, the Zelda encyclopedia
Here are found some of the thoughts I've had about the Zelda series. Enjoy! (I'm assuming people reading this have played and completed Skyward Sword.)
The Holy Temple
In the Zelda series, dungeons are everywhere. Dungeons are where everything distinctive to the Zelda series come together. In the dungeons we have puzzles to solve, monsters to fight, and new places to explore. Many of these dungeons are called "temples". However, there is a difference between dungeons and temples. A few temples appear in Zelda games that have none of the characteristics of dungeons, while some dungeons have none of the characteristics of temples. Some structures are both temples and dungeons. So, if we define a dungeon as some sort of structure filled with traps, puzzles, riddles, and monsters protecting some sort of treasure, how do we define a temple?
The biblical temples had two main functions. Each of them was described as "The House of the Lord". The Temple was where God would reveal Himself to His people. It was where His people could go to feel closer to Him. The Temple was a house of prayer. It was where Heaven meets Earth; is was spiritual high ground. The Temple was truly considered to be sacred ground.
The first function of the Temple was it's use as the house of God. Secondly, the temple was where sacred ceremonies and rituals were performed. So we can see that a temple is not a church or a cathedral. It is not a place of general assembly. Rather, it is a holy place where sacred ceremonies are performed and where the people may go to feel they are entering the presence of God.
The biblical temples are always divided into three distinct areas. There is the Outer Courtyard(s); next there is the Holy Place; and finally, beyond the Veil of the Temple, lies the Most Holy Place, also known as the Holy of Holies.
So, in the Zelda series, a temple would be a place regarded as sacred ground. It would be a structure dedicated to a deity, and sacred ceremonies would be performed in it. Now, I noticed that a lot of the temples in Skyward Sword follow this pattern. I'll talk about them in the order Link visits them.
Isle of the Goddess
The "Holy Place" portion of this temple is the platform made by the Goddess Statue's hands. This place is only visited by Link twice, once while performing a sacred ritual with Zelda, next while praying to the gods of the Triforce near the end of his adventure. The Skyloftian Parrow states that the ability to ride a Loftwing is what separates children from adults. Therefore, this Holy Place can only be visited by mature citizens of Skyloft, and it seems they only come here to perform the sacred ritual. This isn't a place people just waltz into to hang out.
Finally, Link is led through the stone door forming the "Veil" of this temple by Fi. This Chamber of the Sword serves as the "Most Holy Place" of the temple. The only people allowed to pass through the "Veil" are the Chosen Hero, and Gaepora and his predecessors. It is interesting to note that Gaepora and his predecessors are the keepers of the sacred texts and ancient lore, and they are not only capable of entering this Most Holy Place, but they keep knowledge of this place hidden. Considering this, it seems possible to me that Gaepora serves as a sort of high priest for his people. They watch over this Most Holy Place, waiting for the Chosen Hero to appear.
So in summary, this temple is divided into three areas, with certain sacred rituals performed in each part of the temple. And, considering the Isle of the Goddess is part of the Temple of Hylia, it seems obvious that this temple is dedicated to the Goddess Hylia.