This amazing fan theory says yes.
My only complaint about Captain America: Winter Soldier, was there was no lead up to the Hydra reveal in the previous movies. Which is especially weird, because in the first Avengers movie Tony actually DOWNLOADS ALL OF S.H.I.E.L.D.'S SECRETS. That seems like a pretty big one to miss, right?
This theory doesn't totally solve that problem, but it's cool to imagine that the ground work for Winter Soldier were there all along: