On a 2-0 count in a 5-5 tie game in a very offensive environment, it just isn't worth the out. Fukudome is a very patient hitter, and is probably around a 50% chance of walking anyway, especially when considering the batter before walked.
So the Cubs gave up a chance at first and second nobody out to get a runner on second with one out. I don't think I need to tell you that it's easier to get that run in if you have 3 outs left instead of 2.
Plus all chances of a big inning just went out the window. There's a good chance that one run isn't going to seal the deal. But even if it would, I don't think that improved the odds of scoring the one run even. Not at Coors against a pitcher that isn't throwing strikes.
Fangraphs agrees with me, http://www.fangraphs.com/liveplays.aspx?date=2011-04-17&team=Rockies&dh=0&season=2011, saying that the bunt cost the Cubs a 3% chance to win that game, from 56.7% to 53.7%. That doesn't even take into account the favorable 2-0 count that was wasted.
Edit: That was written before the inning unfolded. If we take the benefit of hindsight, in addition to the fact that it obviously didn't work, a walk pushing Sori to second, then the fly gets him to third with 1 out, then scores on the Colvin fly with 2 outs. It's ridiculous to say that's what would have happened, but it's an example of what could have been but didn't get a chance.
Maybe Castro, who would have been up next, and was smoking the ball today, would have given the Cubs a second run that inning.
The Rockies came up in an identical situation in the bottom half of the inning and did not bunt, and it paid off big. If they did bunt the runner would have never moved from second. The Cubs sac bunted their way to a loss. They haven't officially lost yet (I'm writing this as the Rockies are unloading.) Maybe they will win despite the bad decision.