Apple is different from the general rule because it's a company that makes electronic goods (founded 1976, and well known since the 1980s) which later opened a chain of stores (starting in 2001), so the word "Apple" primarily refers to the corporation, not the stores. It's common to refer to "an Apple store" to indicate you're referring to the store rather than something else to do with Apple - "I got it from Apple" could mean you bought it online, while if you heard "I got it from KFC" you'd be more likely assume they went in a restaurant/takeaway (unless they order a lot of food for delivery). It's all about context, and including all information that is necessary while omitting information that could easily be guessed or isn't needed.
You might say "I'm going to get it from the Apple Store" or "I'm going to get it from an Apple Store". The former if there is only one store, or it's assumed you'll go to the nearest one; the latter if there are many stores but you'll choose one for some reason or another, or you don't particularly care which one you go to.
There are different ways of referring to different chains of stores, and it seems to vary from country to country as well. Some stores are referred to with a possessive, like Macy's, Sainsbury's, McDonald's, Walgreen's, etc. Often these look like they're somebody's name. Some other stores aren't referred to like this - a lot of them are initials like KFC, BHS, C&A, etc, but some have other names like Burger King, White Castle, Asda, Walmart, Target, K-Mart, etc. Sometimes there is no consensus or no real logic.