The Red Skull has survived being blown up, worn away into dust, having his energies drained into a small cube and things far worse than anything that Nick Fury can do. The fact that the Red Skull has survived for as long as he has is a testament to how tough he is. He hates Americana and what it stands for, so he hates Nick Fury, and his hate is what fuels his will to survive. In terms of how he downs Fury, that's simple, he uses the Dust of Death. What is the dust of death I hear you ask, well it's a dangerous dust that can be deposited onto it's victims skin through a fake cigarette. Within seconds the victim dies. Sorry Colonel Fury, but you're going down. Another one bights the dust.
A fake cigarette? You think Nick Fury... a guy who has fought GODS is going to be taken down by a FAKE CIGARETTE?
The fuck's wrong with you boy?
Nick Fury isn't exactly a fragile errand boy, and there's a reason he's the guy who is forced to deal with Superheroes... he's the one that has the power to wear them down.
You talk about Red Skull being fueled by hate and it's his willpower that helps him survive. You don't think Fury is going to be dead set on taking out Red Skull too? Fury will see this as an opportunity to rid the world of one of the greatest threads to freedom and democracy, and you can bet on Fury wanting to end Red Skull more than anything in the world.
And Fury has the tools to do so. He's an expert marksman, and a few slugs stuck in Johann Schmidt's brain will but an end to the jackass known as Red Skull.
Oh, and when you say, "The Red Skull has survived being blown up, worn away into dust, having his energies drained into a small cube," do you forget that this isn't a fight to the death? It's a fight to incapacitation, which could mean death or knockout. You're right in saying that Fury has little chance of finishing Red Skull off, as Red Skull psionically transfers his soul to another body after he dies, but as long as Fury can take down Red Skull's current body,
and he can and will, he will walk out victorious.
Fury all day here folks.