willRules
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This could probably go in the questions thread......although I suppose there's lots of room for discussion on this one....
Nothing has been confirmed but I'd guess that Hydra created SHIELD as a sub-faction for it's own gain and the directors of SHIELD, seeking to stop terrorists, came across Hydra and started foiling their own plans. Hydra effectively shot themselves in the foot, not that they care....after all CUT OFF ONE LIMB AND TWO MORE SHALL TAKE IT'S PLACE....HAIL HYDRA!!!!!
It was revealed that SHIELD, amongst many groups was a Hydra organisation, in Secret Warriors #1. I could be wrong but I think it also mentioned how factions of the United States government also fell under the Hydra umbrella, so maybe it's just a simple case of the groups fighting Hydra without realising Hydra technically owns them.