I'm expecting a third baby "any day now". My two ex utero children feel expensive at times, but I can guarantee you that I'm not spending anywhere close to the yearly estimate of that calculator. When our new baby is born my wife is going to stop working full time to take care of the kids and do some freelancing. When those paychecks stop it will "cost" us some money, but she's still going to be very productive with non-baby activities and likely still earning some income.
As with many financial articles, I'm left wondering "what are they spending all that money on???". The top rated comment to that CNN article, by "Guest", sums up my perspective quite well:
The hardest financial way for a parent to raise a kid? To try and live up to the American Upper Class ideal with a bedroom for every child, multiple bathrooms, car payments, smartphone plans for every teen, all the cable TV channels, all the brand name clothes, etc., etc., etc..
As a parent, when you quit being materialistic, and help your kids be free of materialism - it is amazing how much more affordable it is to raise children!
Here's an article from 2007 that mentions some flaws in the USDA's methodology.