I've often wondered about this. The answer appears to be yes, with caveats. Obviously taking mass transit and shopping local stores is better. And what of the drive-to-independent-bookstore vs. shop-at-Amazon dilemma?*
Then there's the greenest solution of all: just quit buying crap. My problem is that I find it far more pleasant to buy things online than to go out shopping. I prefer to wear clothes that don't even fit to the prospect of being in an actual store, being attended to (god help me) by a salesperson, and trying things on. So for me, going out to shop may be greener. I'm more likely to leave empty-handed, and probably to decide not to go in the first place.
*UPDATE: Looking at the article again (i.e. actually reading instead of skimming), I see that buying books at Amazon is not so green. You only want to buy from aggregators that don't ship out of central warehouses, which is not the case with Amazon's "media" products.