1. VGChartz publicly makes corrections and updates. NPD hides any changes it makes. Thus people feel VGChartz data is unreliable because it changes and never see NPD information vary. (And everyone remembers the high-profile corrections).
2. VGChartz is free. NPD costs money. Thus, to some VGChartz is worthless while NPD is valuable.
3. VGChartz method is documented. NPD is proprietary and hidden. So people don't trust what they know about but accept on faith what they don't. (And ignore counterintuitive information like NPD has no current generation Wal-Mart or Toys R Us data -- which could be skewing its numbers if it is using old models).
I have seen VGChartz used everywhere from G4's X-Play to the NY Times, so there is some acceptance of it. Meanwhile, Wikipedia can't even get the sales for the Intellivision correct, based on the source that is cited in the article on its page -- so it is not perfect either.
Mike from Morgantown