Bookstores and things are desirable to local residents but are less profitable than other prospective tenants once the area has high traffic. The bookstore can't afford the higher rent but a Starbucks or something can. The landlord is willing to take a short-term vacancy for a long-term higher paying tenant.
Therefore, if you want local bookstores you need enough supply of commercial real estate to keep the rents at a level the bookstore can afford, or they'll get replaced by chains.
Whether it's a franchise or not isn't really the issue.
It's that something like a coffee shop can do a ton of business in a high traffic area, and so can pay a higher rent than a local bookstore. So if you only have enough rental units for one of them, the coffee shop is going to bid higher. Which means if you want to have both, you need enough units to exist for both.
Also, you're not actually trying to lose the coffee shop. You want to have both.
Therefore, if you want local bookstores you need enough supply of commercial real estate to keep the rents at a level the bookstore can afford, or they'll get replaced by chains.