I thought the same thing too, for years. Then one day I was watching it with someone and it all just kind of fell into place for me. It's like "stoner funny", I think. It's funny in that it's unlike anything ever created in cinema, and it's actors and actresses all shine in their notable roles. It's very akin to Howard Hawks' adaptation of The Big Sleep, in that it has this confusing, meandering plot that's too inexplicably compelling to stop watching. Jeff Bridges, John Goodman and Philip Seymour Hoffman have these complete fucking oddball roles unlike anything else they've ever played, and yet they nail it perfectly.
That part when the Dude is sitting in his bathtub smoking a joint, hearing the answering machine message about his car being found and then getting a marmot thrown in his tub by the Nazis makes me almost piss my pants every time I see it. And I can't even figure out why