Remember that FLGS are totally a dice roll. At least some of them are run by gamers who don't know how to run a business well...
Regardless of how well they can run the business, sometimes it just has to do with the local market. In smaller towns, these days Magic and comics, and other collectible games, are the major money-makers; board games come in second; and rpg books and accessories are just a tiny percentage of sales, and so they just don't warrant a lot of shelf space.