Bin Laden was behind a push to overthrow the Saudis. His group managed to successfully operate within Saudi Arabia for some time. They were a secret society because openness would make them able to be caught and prosecuted for treason. Regarding 9/11, sure the Saudis wanted to preserve their own regime, but that was only because someone behind the 9/11 attacks was also working to overthrow them.
AQ is and was not the only grp. ISIS is another, more recent & infamous one. There are many other grps. But it’s more like one islamic set officially in charge of a country fighting another which is not.