Experimental evidence suggests that people gain significant psychological satisfaction from exercising punishment mechanisms in multi-stage prisoners dilemma situations, even when doing so is worse for punisher than the punished. I'd guess that most players dislike certain deck attributes (un-original, un-fun, cheap strategy, too difficult, too many rares) enough to exercise the thumbs down option. Honestly, considering there's no direct harm to the player voting, I'm surprised there are any up votes at all.
Clearly auto-up voting is optimal from a monetary perspective, but I'd guess that most players gain more enjoyment from casting down votes than from a slight uptick in coins.
Personally I try to vote up any deck that doesn't seem "standard" or "obvious", but my definition of those qualities certainly shifts with my mood (and it doesn't stop me from making un-original decks of my own).