It's all taste. When people say "you don't understand" what they mean is "you have different tastes than me and you're a dumbass." Just say,"yeah, I do understand. I just don't like them. They're not my cup of tea." Same thing with people who don't like jazz or classical. It's sometimes not that they don't understand (although sometimes this is the case, yet I don't think you are a person who doesn't get it, you seem to be very intelligent) it's simply not their thing. A lot of jazz I can't stand because it is so difficult to find emotion underneath the virtuosity of some of the greats. That doesn't mean that I don't get it. I just don't like it. Simple.
EDIT: I'm not to much into Meshuggah because I can't stand how fucking slow they play. Tool, however, are not that ambiguous. They are pretty intelligent, and have great themes in their songs, like nihilism for example in Enema. But they aren't overly subtle, or extremely deep.