It's a gamble, but so are half the other cards. Besides, the resources they spend dealing with your Doomsayer would have been better spent developing their board. Sometimes you play it by itself. Take the last game in the Trump Freeze Mage guide. He was two turns away from having the mana to finish off the hunter, and he had a read that the hunter was definitely going to play Savannah Highmane on turn six. So he Doomsayered on an empty board (crazy, right?). Sure enough, the hunter passed his turn. Then he Doomsayered a second time in a row. This time the hunter realized he was on the clock and (sure enough) played his Highmane. By then it was too late and the hunter ultimately lost.
The Frost Nova by itself already provides value because it stalls the opponent. When the Doomsayer hits, however, it forces the opponent to redevelop from scratch, and that's going to buy a few more turns. The whole idea is to stall, and Doomsayer does that very effectively, whether it's by forcing the opponent to waste a turn dealing with the Doomsayer or by resetting the board state.