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So alot of people believe that the temple was created, or is somehow associated with Dharma, due to the logo on particular maps throughout the series. Well, basically everything i have to say below is mostly assumptions, but it all makes sense, and it's not too hard to imagine such a concept either.
When the Dharma guys came, they built their village on the temple (for a reason i'll theories below), and then they adjust certain things, in order to in some ways control the temple. Horace's house had the secret door, with the sinkhole that presumably leads to the temple or the tunnels. There is also a recently cemented wall connecting one of the tunnels, and horace's basement (which richard bashes in most bodaciously in the S5 finale.) This means that DI must have a particular interest in the Temple, especially if they decide to base themselves there.
My guess is, (and this is a big guess) that all their scientic discoveries, theories, goals, etc, are based on something inside the temple. Some sort of power that (from a scientists' point of view) is highly essential to the other properties of the island, such as the electromagnetism and the time wheel.
Think aout it, it MUST be important if they decide to build themselves on top of the tunnels, and with the knowledge of them being there, as they made the top house (horace's) just on top of one of the tunnels. Maybe the reason why the others and DI fell out with each other in the first place is because DI decided to live on the precious tunnels.
This is why the temple has a dharma logo. Because DI were interested in the temple.