The Matrix bluray doesn't have a blanket green tint across the whole movie; in fact the 'real world' scenes have pretty much the same color timing as previous releases. Scenes set in the matrix itself always had a slight green tint, but the bluray ramps this up to 11 and makes some other questionable color changes to these scenes.
Here are some good examples of what I'm talking about: (EDIT: It should be noted that although the screens on this page all from DVD releases, the most recent DVD has the same color timing as the bluray)
http://www.dvdactive.com/editorial/articles/the-matrix-visual-comparison.html