Well, their skill
shows in good sound and clever songwriting
You don't have to like them, but if you listen to the songs on for instance, Natural Born Chaos, they're very cleverly composed and executed. It's very clever and good music. Catchy grooves, good melodies.
What I'm trying to say is that you can argue about how much you like them, but you can't doubt their skill and talent. For instance Mozart, it's simply a fact that he's a genius composer, it requires incredible talent to compose the music he wrote, regardless of the fact whether you enjoy his music or not.
Same with Tool, they're incredibly talented, but their music just doesn't do a lot for me.