Nick Fury's not a bad guy, he'd have nothing to gain from being a bad guy. He has his own motives, and he does what he thinks is right. We know he's more liberal than someone like General Ross, or Colonel Wraith because he said he voted for Nader, and it shows. He took away the supposed need to throw countless lives away by giving the Supersoldier Program a budget boost. Now, regardless of this, he is still a General (except in USP, i suppose... :wink: ) and he thinks like a general. He does what he needs to do, and he has screwed up, but not everything is his fault.
Another thing that should be pointed out is that OZ was being worked on before Nick Fury became Director of SHIELD. Nick Fury was at that point an Agent, a pawn of SHIELD, he very possibly wasn't involved in the process of creating superhumans before he ascended to that position. He read the file on Banner, got his idea for the Ultimates, and started hiring. He is not responsible for all the crazy super people we had in Ultimate Six, SHIELD is, Fury isn't. Fury held them without trial because they are in all technicalities not humans, and the same laws do Not apply to them. Yes, the government wanted people to develop supersoldier serum, but I bet they never authorized testing on humans. They did test on humans, and those people were no longer protected by the constitution, because they were illegally in existance. I dont see any of that as Nick Fury's fault.
My biggest problem with him is that he is pushing around the world with his Ultimates, and I do think he's had a little bit of an ego trip. Regardless of who Henry Pym was or what people perceived him to be, the old Nick Fury wouldn't ignore flying death robots... Now he's using the team to ensure American power, and if you had the Ultimates, why wouldn't you use them to help fight an otherwise catastrophic situation? I would. Is it right, probably not. Does it make sense? yes. Nick Fury runs by Logic and Politics, and little else.
I don't think he's being malevolent.