FontBook turns off-- Illustrator keeps on?!?


Why are fonts still visible and usable in Illustrator CS2 when I have turned them off in FontBook?!? I'm trying to limit the gigantic list, and nothing seems to be able to do that.
I'm running 10.4.2 and Illus CS2 12.0.0 on an ibook g4 1.42GHz.
I'm new to Tiger, so while I'm at it, what are the good font management programs? Is FontBook sufficient? What about type display programs.. similar to TypeSet?