Word around the web is that Hydra is behind The Rising Tide.
That doesn't exactly make it any clearer.
In the 2nd episode, which mentions Hydra, Skye makes a speech about 100 people having 1% of the answer (i.e. multiple heads of the mythological Hydra).
Good grief, what an enormous stretch. She was talking about crowdsourcing, about the increasingly popular -- and populist -- notion that the collective expertise and inspiration of the public as a whole can solve any problem. It's exactly the mentality that would be expressed by a member of a group like the Rising Tide or the real-life groups it's based on. Plus it was presented as a positive idea in the context of the story, the mindset that saved everyone's lives in the climax when they worked together, so it's strange to read it as some sinister portent of evil.
Besides, the key thing about the Hydra's heads in mythology isn't simply that there are many of them, but that they multiply -- if one is cut off, two more will spawn. Which is, in fact, the intent behind the organization HYDRA's choice of the name, to convey the idea of their indestructibility and the futility of any attempt to defeat them. So it's a different concept altogether from the one that Skye was expressing.