I think the real issue is that the play has to drive revenue. A store that provides playing area has to derive some sales or other income from providing that space. It could be anything from a table fee to a soda or snack to cards or other game components. When I have considered running games in a store, I figured that I would require the players to buy something for the game from that store as a sort of admission price. It's a business. A game store has to make money to stay open.
A table fee could be the solution to the problem without making it personal or whatever. I think $1 an hour (or session or day or whatever) per player is perfectly acceptable. Buying something in the store could get free play for the day. But, there has to be some respect for the store owner.
One of my former FLGSs closed a few years ago. An incident I remember is that some of the players were mad that a certain board game cost $5 more in the FLGS than in the big box store down the road. So, these fools went down the street, bought the game for $5 less; and then brought it back to the FLGS to play it. And they mistakenly thought the FLGS owner was trying to take advantage of them. One of the players worked at the FLGS. If I had been that owner, I would have fired him and banned the others; or at least banned them from playing that game in that space. As it was, the FLGS closed shortly afterward. I think people in general - and gamers in particular - do not think big or long-term.
You gotta pay to play. If you don't buy from that FLGS today, it might not be there tomorrow.