The Illuminatus Trilogy is a couple of guys getting stoned and screwing around with various goofy ideas. Like a lot of postmodern stuff, it doesn't take much of anything, especially its subject seriously.
Foucault's Pendulum is a very smart guy who knows a lot, pointing out that, if you peel an onion you won't find anything in the center.
I think there's rather more to the Illuminatus trilogy than that. And I say that as big fan of Eco who has enjoyed his deeply obscure stuff as well as his more well-known works.
Illuminatus! is a work of satire, so it not taking itself seriously is part of the point. If you want to really get something out of it you have look beyond the psychedelic sillyness, and read up one some of the countless philosophical/occult concepts and historical oddities referenced in the story.
Foucault's Pendulum is a very smart guy who knows a lot, pointing out that, if you peel an onion you won't find anything in the center.