If they offered the exact same warranty and support as a new camera, why would anyone buy new? To save a shutter rated to 150,000+ shots a few hundred clicks? To avoid a scratch or two? The warranty is that way to differentiate the two options. Pay $1999 for it new, or save $400 and take a slightly higher risk of 90 days vs 365.
Also, note that it's not Nikon in charge of the warranty (like Canon does with their refurbished stuff). It's a 90-day B+H warranty
people avoid refurbished just for the fact that it's not New. it's pretty noticeable on SD.
look at the refurbed Oly cameras. People still buy new even if it's got the 1 year warranty.