With Captain America The Winter Soldier set for release in theaters, Robert Redford was casted as the senior leader of SHIELD, he then spilled the beans that his character is actually a villain. This may trigger a possible twist but it would help make sense why S.H.I.E.L.D. was using the Tesseract to make weapons like HYDRA did in Captain America The First Avenger.
Afterall throughout the Marvel comics, Nick Fury has always been the director of SHIELD meaning leader and commander who runs the entire organization. In the Avengers film after the attack on the Helicarrier, Fury told Tony and Steve that it was never his idea to use the cube to make weapons at all. This could mean that Redford's character could be the explaination to just that which rumors him to be none other than Captain America's arch enemy:
The Red Skull
In Avengers Earth's Mightiest Heroes, the Red Skull hides himself under a mask as Dell Rusk and was said by Captain America that he destroys good people by turning friends against one another. But then again, you never know.