We can quibble over whether or not making customers pay to use the space is a good business decision, but in the end the store management has the right to make its own decisions on the use of the space.
Of course, some of those decisions might bring a third party, such as WotC, into this. It would be within WotC's right to set up rules for how much of a fee may be allowed at a WWDDGD event, or even disallow one at all. Once a store decides to run the event, they have to follow those rules.
I have dealt with a few organized play programs over my gaming career. Typically companies understand and allow for reasonable "table fees" to be allowed for events. Most games stores are running on very thin margins and space costs money to have and maintain.
That said, they have also become wary of stores with ethically questionable policies. I know that back when WizKids was at its height, many of their prize packs had very high eBay values. You would see stores try to do all sorts of things so they got these prize packs to sell on eBay, even putting them on eBay before the event in question. I have heard of, and even seen in some cases, stores move events just before the event in question*, be people's home addresses, require large entry fees (I have heard of $20 entry fees), or make bad excuses at the event for not running it.
The flip side of this is that game stores have also got the short end of the stick in some areas. It was not uncommon to have "carpet baggers" show up with a killer tournament deck/army/character bought off of the discount internet sites, show up to crush the local "for fun" crowd and walk away with the prizes without spending a dime in the store. A good percentage of the time you would see that person with 3 or 4 of the prizes up on eBay, cashing in on it. I know at least one person who paid his rent doing this on some months.
To counter this, I know some stores set up minimal tournament fees. They would charge $5 or less to play. Often, they would take the fees and use it to purchase product at the store to add to prizes (typcially everyone walked away with something at these events).
Now, obviously Worldwide D&D Gameday doesn't quite attract this type of person. The giveaways aren't particularly valuable. Still, they certainly see the sort of person who values the game stores enough to want to come out and play, but not enough to actually spend money at the stores so they can survive to give you a place to play in these events.
Raise your hand if you would have liked to play in any of the WWDDGD events but didn't have a local game store to play in. Keep it raised if you had one that would have run these events (and you were willing to go to) but it closed. Keep it raised still if you didn't support your store while they were around.
I think most companies would be very upset at a game store that required a $20 purchase to play. However, those same companies would not have a problem with a requirement for a $5 or less purchase to play (assuming it was clearly advertised so potential players could be prepared).
* I personally had a store change I event I had checked less than an hour before it was to occur. I checked before my 45 minute drive to the Lancaster area, only to find the store locked as tight as a drum on my arrival.