I love Lynch to bits because he refuses to be obvious and structured. In my opinion film is not a good medium for conventional storytelling. Drive could serve as a pretty good example of that actually. Ignoring for a moment that I didn't like it, I know that a lot of people did. I'm pretty sure they wouldn't care for it if you'd just write down what happens in the film and hand it to them, though. The story is not what makes it a good experience.
Films have a powerful way of communicating images but as far as actual story goes they're fairly mediocre and overly reliant on plot (thus why the book is almost always better when it comes to adaptations). Their strengths, rather, lie mainly in emotional and visual manipulation, and the way they shape characters. Lynch is one of few filmmakers who understands this and uses it to his advantage. I think I've read that the script for Eraserhead was less than 20 pages long. His focus clearly lies elsewhere. In that particular film, for instance, he's preoccupied with showcasing the main character's claustrophobia and fear for everyday life on the screen. All the abstract weirdness and symbolism in his films has more than one assigned meaning, but it still makes intellectual sense. He's a visual storyteller rather than a literary one. I think Eraserhead, Twin Peaks and Mulholland Drive in particular are great examples of this.
I think most people accuse his movies of not making sense because they feel they need some kind of familiar narrative structure to fall back on in order to be comfortable. I also suspect that it's completely unnecessary and, fairly often, gets in the way of true filmmaking.