Yup…remember being shocked when that game came out…was prior to 911. They sold the game as a web of conspiracies so the average joe probably didn't pay much attention…but it's loaded with everything. A lot of the little books and snippets you read contain much more…stuff on the Knights Templar, for instance.
At the end, however, they portray the Illuminati as something more akin to the masons…and they're largely perceived as good guys trying to stop a rogue member from doing terrible stuff. They could've gotten away with more truth there…but all in all, it's pretty well done, and nobody will ever get away with including this kind of content in game ever again, unless it's inserted as an object of ridicule.