Larger sensors do not have a proportionately less amount of noise than smaller sensors, relative to area, which is light gathering ability. In other words, a sensor that is 23 times larger does not have that much less noise. As size drops, efficiency (per unit of area) goes *up*. More on this below.
To illustrate, imagine a 200 MP camera, let's call it ACS (I love Hubble!). If we compared 100% crops from ACS and D3, and the ACS had three times more noise, this flawed comparison would indicate that the D3 is better. Now imagine resizing those 200 megapixels down to just 12. The reduction in noise would be far greater than just a magnitude of 3, and the D3 would appear to be much noisier.
Now change the illustration from ACS to 1Ds3 and 200 megapixels to 21. See how it reduces apparent noise?
The comparison is further flawed by using inequal exposures (1/40 vs. 1/50), not accounting for Nikon's black point clipping (not apparent in their image anyway) or especially their chroma desaturation.
In real life, are you going to crop a 4x6 out of your 21 MP image? Or are you going to resize it to 4x6 for printing? (People do all sorts of things online that they wouldn't in real life.)
Imagine someone took the Canon 5D sensor and wanted to make a 1/1.7" digicam out of it. So they got an exacto knife out and cut the center 37 square mm out of the 5D sensor and put it in a little camera. On that area, the 5D had 0.5 megapixels. But they're *good* pixels. If you look at the 0.5 MP image at 100%, it's clean and nice, whereas the 12 MP G9 image at 100% looks very noisey. Now resize the 12 MP G9 down to 0.5 MP... the 5D crop looks terrible in comparison. If you don't have an exacto knife, you can do the same experiment by cropping the center 0.5 MP in photoshop out of the Canon 5D. Thus proving that sensors can have *more* pixels in the same area to capture more light and less noise.
If they made the 5D with the same pixels as the digicam, it would have 280 megapixels. And by the time you resize that back down to 12 MP to compare with the real-life 5D, it would have a lot less noise. Obviously, they would if they could. But it dispels the fear that more pixels will mean more noise.