Lysandre hated that through war and misuse of resources humanity was slowly hurtling the world towards its demise, and after years of trying to use his position of power and wealth to better the world to little avail, in an extremist move decided to kill off most sentient life and micromanage what little was left from there. His scientists believed in his goals as well, and basically everything Flare does throughout the game is done in the name of research or resource gathering to power the Ultimate Weapon in the final scenario with them, which would be used to those ends.
Everyone who joined him either did it because Team Flare had stylin' outfits and looked cool, wanted to be in this exclusive group run by the powerful entrepreneur that was Lysandre, or knew about their real goals and didn't want to be one of the people to die.
