My theory is just that the people are just so caught up in the thought that Pulse is evil or essentially uninhabitable. The people have always had a great fear of Pulse, and even if the fear of fal'Cie is gone, the people probably still remember the assault on Cocoon by Pulse monsters from the first game.

There is also the possibility that the people just all have the belief that there has to be a Cocoon since there always was. That's probably why Hope tried to make a man-made fal'Cie, that's how things have always been run before. Maybe even Hope is just under the assumption that Cocoon has to exist, or it could just be measure to provide a safe place for those who refuse to live on Pulse to live.

Part of me thinks that some of the issues with what the Academy is doing has to do with the fact that Hope has his hands on everything, even throughout time. Rather than leaving a foundation for others to build on based on their own experiences that have progressed from the times of XIII, they continually follow the vision of a man who (although brilliant) may not have a proper perspective to bring a better solution.