It wouldn't matter whether D&D was edging out PF or the other way around. There are enough other RPGs out there that the two of them even being close means that neither likely has fifty percent of the RPG market. Even if you assume non-D&D/non-PF games make up only 5% of the RPG market with 48% of the market belonging to D&D and only 47% to PF, it's a radical change from the former dominance of the greater portion of the RPG market. It's just as likely that 10% or even 20% are non-D&D/non-PF RPGs, which leaves even less of the pie to be split by the two leaders.
As to the FLGS D&D sales over the past four years, Amazon pre-orders of gift sets vastly cut into FLGS sales at the opening of the new edition (something that was barely on the radar with 3.0 and not too troublesome with the release of 3.5). Any money diverted to DDI is consumer spending on D&D that FLGSs have no chance to realize. You don't need a link to understand this and comparison of D&D/PF nor comparison of 4.0/3.X sales figures aren't relavant to this separate but related point. The question becomes, since D&D is a diminishing source of revenue for FLGSs, as the publisher diverts the revenue stream online, what do the FLGSs do to replace the revenues?
One avenue would be to rent time on electronic gametables. Selling the minis and programmable bases, and having the tables in-store to accomodate them, might be a short term revenue replacement (until such tables become generally affordable).
I found one of my posts about my estimates for RPG marketshare.
http://www.enworld.org/forum/5622002-post458.html
Basically, of the approx. 4,000,000 (or less) of so-called "regular" players of TRPGs,
at least 2,000,000, or 50%, regularly play 4th edition (admittedly by my skewed, unscientific, probably biased calculations). A better guess would be 60% 4e, 30% Pathfinder/3.5 (with the exact Pathfinder/3.5 ratio possibly being as high as 50/50), 10% other. This is for regular, monthly players, and not sales.
I regularly see 4 4e groups for every Pathfinder/3.5, but I know some others have witnessed as much as the complete reverse. Thus I tried to be more conservative with my guess; thus the 2:1 split (4e

athfinder/3.5 ratio). I also assume (perhaps wrongly) that for every 3e group that moved to Pathfinder, another group probably stayed with 3.5.
As far as FLGS, WotC seems to be responding by trying to draw traffic through with Encounters. Also, they've been focusing on exclusive adventures, etc. In fact, now they've got a product (Mordenkainen's Magnificent Emporium) that will be FLGS exclusive!
Unfortunately, much like Borders, FLGS may become a thing of the past despite WotC's best efforts.