I think the idea that if you don't like Tool, you just don't understand them is weak and insipid. I don't like Tool because they are tame, boring, and slightly generic for their style. Aenima was ok, but half the album was filler. Lateralus was my pick for worst album of the year it came out, it was beyond boring. The songs went nowhere, there was practically no deviation between songs, and it was way too long. Compare it to say, Maudlin of the Well's releases from 2001, Bath and Leaving Your Body Map, and it's almost absurdly dull in comparison.
Also, Dredg rereleased their '98 release in 2001, Leitmotif. It is FAR better than anything Tool has ever done in a very similar style. The drumming is better, the singing is better, and the song structures and guitars are INFINITELY better. It's also less than 40 minutes long, so it doesn't have time to get boring. Overall, it's 10 tracks, but mostly 5 songs. Their 2002 release, El Cielo, is also similar at times to Tool but absolutely infinitely superior. Better lyrics, better themes, better songwriting, better drumming, better guitars, better electronics, better album flow, etc...
Tool are almost absurdly overrated. They are beyond horrible live, their stage show featured a period that was over an hour long of a repeated noise while naked people hung from ropes. Color me unimpressed. Their music is dull and uninteresting for the most part, but they shine at others when you don't pay attention to their lyrics.
For intelligent progressive music, I would much rather listen to Maudlin of the Well, Ephel Duath, Dredg, Sleepytime Gorilla Museum, The Mars Volta, and many other newer prog bands that just absolutely shit on everything Tool has ever done. Listen to Sleepytime Gorilla Museum, with their one string bass, homemade instruments, and bizarre songstructures and vocals... it will make you realize that Tool are just watered-down prog, tailored for the masses. Just like all throughout rock history, mainstream bands stand on the advances that lesser known bands achieved simply because of marketing and peer pressure. There are a few exceptions, such as Radiohead's monumental OK Computer and The Afghan Whig's godlike Black Love... but for the most part, even the best mainstream bands such as Radiohead pilfer the underground (Kid A for example, Ok Computer was something of a fluke).