Yes, he is an antagonist, but he isn't a bad guy! It's just I see these things people say where they depict him as a villain. Here are my reasons.
1. Everything he does in the game, he does for the good of the people. He tries to defeat Sephiroth because he's trying to destroy the world.
2. (Here comes a spoiler if you are new in the game or you suck) He's also trying to get Sephiroth for a personal vendetta because hey, Sephy DID kill Rufus's dad.
3. Rufus also goes after Weapon when it's doin' its thing, again, because Weapon is a danger to the people.
4. (Spoiler) The Huge Materia things, he's just trying to destroy Meteor before it destroys the population.
5. During his brief skirmish with Cloud, he was defending himself! Here was Cloud, this insano with a huge sword, prepared to kill Rufus just because he was the President of Shinra!
6. Rufus fled at the end of the fight not because he's a coward, but because who would lead Shinra if he died? Heidegger? Scarlet? I don't think he wanted those idiots running the world.
7. When he says he'll control the world with fear, he doesn't mean in a Hitler way. I think it may be a misunderstood translation, but listen to what he says after that. "Work at Shinra, get your pay. IF A TERRORIST ATTACKS, the Shinra Army will help you." He'll control the world by being the savior of people's fears.
8. Rufus never actually says that he wants Cloud's death as an objective. If you do the Yuffie sidequest (spoiler) and the Turks have just done away with Don Corneo, Reno gets a call from HEIDEGGER to find Cloud. Not Rufus.
9. (big spoiler) When Rufus takes the Junon gun, or Sister Ray*, and puts it in Midgar, you see his objectives? He's not trying to kill Cloud! He inadvertantly HELPS Cloud by destroying the barrier! So in my opinion, Rufus doesn't deserve the dogging he gets!
*Funny thing about Sister Ray, by the way. After the gun's in Midgar, Scarlet names the gun Sister Ray. But (spoiler) when Tifa is running away from Scarlet and the soldiers on the gun, you see that the words "Sister Ray" are already on the gun!