If I understand the economics right, that's generally to dump the gamers out and use the space for something more profitable. FLGS may operate as commercial entities, but they're not Limited Liability Corporations (usually), and have no responsibility, legal or otherwise, to maximize profit at the cost of anything else the owner might prioritize. If that includes banning mega-corp games or D&D rip-offs, then that is as they will.
While i'm not a tax expert, one could percieve gaming space as "marketing" expenses. Having players in a store is like having a captive audience for your merchandise. Less obtrusive than a billboard, they will be surrounded by product. It's also a microcosm focus group for a given area. A wise owner (or purchaser) will listen in or sit in with the players of any game system, from CCG to RPG, and find out what his patrons want and gauge interest in upcoming products.
A well filled out gaming space also looks good to new customers, provided they are given prompt service and don't feel less prioritized than the regulars.
Also with gaming space, you have a chance to offer profitable food/snack and drink sales.