I think the reason Paizo doesn't really care so much about the FLGS, is because most of its fandom is made up of current gamers. I have no idea how many new gamers Pathfinder has brought into the hobby, but, considering efforts like WOTC's Adventurers League, I'd say it's a lot less than what WOTC has done. I think Paizo has essentially cannibalized the 3e gamer fandom.
The whole point of Pathfinder is that it's a continuation of 3.5: not just a chance to keep playing 3.5 (which could anyway), but a chance to buy validation of your loyalty to 3.5 by wallet-voting for your 'team.' It's a successful business model for Paizo, in part because they are relatively small and agile, able to keep feeding their fanbase what they need to feel validated, and able to do very well off that kind of volume, in part because they walked away from their arrangement with WotC with a juicy mailing list of the game's most dedicated fans. All of which, yes, points to established fans as their audience.
However, the Pathfinder Society's zeal is not limited by business models, and they do make an extraordinary effort to get the game out there in organized play. They hit conventions, stores, trawl for new gamers in person and on-line. At least around here (SF bay area) they seem to put even more effort into it than the AL.
Even something like 5e is probably more beneficial for bringing new gamers to Pathfinder than, say, something like Pathfinder Society. People start out in the hobby with D&D. Then they move on to Pathfinder or whatever other game. But D&D is the gateway game.
D&D is very much a gateway to the hobby. Pathfinder is very much the same gateway. It's just a matter of whether you walk into a store where PFS is running a table or one where Encounters is happening that night. You say you want to try D&D, the Pathfinder guys will introduce you to the 'real' D&D, as readily as AL will to the official. Whether you start with 5e or Pathfinder, you're likely to have a very similar experience of and reaction to they hobby. (No Pathfinder DM is going to throw the whole universe of rules bloat at a new player, for instance.)
Take away D&D, and ten years, fifteen years down the road, simple attrition will sink most of the RPG companies out there.
D&D shows no sign of going away, and, even if Hasbro makes it go away, the d20 OGL is still there, and clones can take up the slack. When people go looking for D&D they'll hear 'oh, there's a Pathfinder/13A/whatever-a-5e-clone-might-be-called' game running at such-and-such store, between M:tG tournaments,' try it out, and probably hate it, but maybe not, maybe they'll be another new instant fan - and the hobby will limp along like always, tiny, but dedicated.