If Apple's intention had actually been a noble one, it would seem odd that they didn't make more of that at the time.
There are arguments for things such as retail price-fixing, but they aren't all one-sided, and some of them are less solid on the net than with physical stores.
Having a small bookshop not being undercut on popular titles by a bigger retailer does help avoid a market dominated by big stores, or where supermarkets selling bestsellers at little profit make small stores uneconomic, but in that situation customers are effectively being forced to subsidise a small store even if they're unlikely to buy anything but the bestsellers.
On the internet, there isn't the same kind of obvious convenience benefit from having multiple stores that there is in real life in having a decent small bookshop in towns too small for a large chain to bother with, even if there may be competition benefits from staving off a monopoly.
The article does cover some important issues, but it does seem to be let down somewhat by an eagerness to ascribe anything good to Apple-led competition, including stuff like having newer versions of Kindles, as if that wouldn't have happened nearly as quickly otherwise.
And is it really impossible to use a Kindle to read ebooks other than ones Amazon sell (should Amazon have to support any competing DRM system, for example)?
Also: "Unchecked free-riding could doom independent bookstores, and their demise would drastically reduce the range of books published and sold. Marketing studies show that, beyond the bestseller list, the main way people discover new authors and “mid-list” books is by browsing in a store."
does seem to be risking a logical fallacy.
1970s-man: "Cheques are the most common way of people buying expensive goods.Therefore in a world with no cheques, far lower sales of expensive goods would be expected."