Most of the funding for the campaign came via Saudi Arabian citizens [0], and they have absolutely benefited from the change in political power in the Middle East.
Al-Qaeda is larger and their allies in Afghanistan have further consolidated their rule. I might not call that "better off" but it's certainly in the direction bin Laden wanted things to go.
[0] https://web.archive.org/web/20060311045338/http://news.bbc.c...