One is that I kinda resent having to pay to play. There are other stores that have similar set-ups, are far more organised and don't charge. Why should I pay there when I can go to another store and not pay anything?
Well, the obvious answer is... if there isn't a good reason, why not go to the other store?
Presumably this store is expecting that the environment the offer - whether due to familiarity, location, convenience, atmosphere, etc - is worth paying the price.
For myself, I probably wouldn't pay to use a game store on a regular basis, simply because I generally game with friends as people's houses. For those without that option, the store wants some compensation for the use of their space, and it isn't an unreasonable concern. I
have paid in the past in order to attend special events or game days or the like, and that seems fair.
In the end, if the price doesn't seem reasonable to you, you don't need to game there. That doesn't mean there is fault to be found in your decision or the stores - they are offering a product you don't feel is worth the price, and so you decline to purchase it. You are disappointed because they gave it away for free previously, and that's fair - but they are under no obligation to do so, and given the current economic environment and the difficulty of running game stores in the first place, their attempt to improve their profits is perfectly reasonable.