Properly because its not that good of a game.
Well I shouldn't say that. As far as puzzle games goes it's decent. With that said it's a puzzle game. They typically don't have as big of an appeal as platforms or shoot 'em ups do. In the end its always about demand. Rarity or age doesn't equal price.
Take a look at Earthbound. According to Price Charting, four CIB copies of Earthbound sell every week at an average price of 400 US dollars, and three loose copies a day @ 126 US dollars. On VGCollect there's almost 300 people who have it in their collection. It is by no means rare. Compare this to Chase the Chuck Wagon on Atari 2600. Last year there were only two copies sold complete in box @ $550 and two loose copies sold a month @ $88. On CGCollect there are only four people who have it in their collection.
Chase the Chuck Wagon is far rarer than Earthbound but comparatively the prices are much lower. Because there isn't as much interest in the Atari 2600 right now there's no demand to drive up the prices. Price Charting isn't 100% accurate of course, but their figures give you a decent ballpark idea.
Unfortunately because Wario's Woods isn't main stream enough or wasn't excessively great in any way the cost is rightfully low. And as mentioned above it's not super, super, super rare either.