It seems that your question isn't so much "why do people vote things down" as it's "why did these reasonable questions/comments get voted down".
Perhaps if you specified which nodes you think got voted down for no discernable reason, we could tell you why we (hypothetically) would (or would not have) voted them down.
It could be random... Once, I posted a reasonable question, and gave a flippant reply to one of the answers. I was surprised to see the reps of both the original question and the flippant reply shoot up over $NORM for no discernable reason -- so much so, I even asked (fruitlessly) why the reply was voted up so much! If flippant comments can have large meaningless reps, I suppose good posts may end up with large meaningless negative reps.
But I could be wrong...