Is it really not obvious what the advantage is? It's a huge advantage: to listen to music on headphones with your shiny new iPhone, you'll have to either buy some shiny new Beats headphones from Apple for $300, or to use non-Apple headphones you'll have to buy some kind of dongle adapter for $29.95. This is a giant advantage for Apple because it'll improve their profits.
The advantage to you is that you can feel warm and fuzzy about being a mindless Apple consumer and having a shiny new iDevice that costs a fortune and only works with other iDevices and forces you to buy new headphones. People like to feel like they're part of an elite in-group.
It's very simple: if you don't like the way Apple does business and treats you as a customer, then don't buy their product. The only reason they're able to get away with this kind of thing (using non-standard connectors is something they've been doing a long time) is because people line up like lemmings to buy their iDevices. If you buy an iPhone with no headphone jack, you really have no right to complain about it being missing; it isn't a surprise at this point.
I don't know how anyone could see those comments as favoring Apple, diminishing the problems, or somehow seeing them as acceptable.
I guess if you start out with the assumption that Gruber is an Apple partisan and nothing more, it's easy to read anything you want into his words.
https://news.ycombinator.com/item?id=7013002
[EDIT: The link above gives a few quick examples of particularly biting criticism against Apple by John Gruber. Not sure what I've said here that's so objectionable -- perhaps one of you could post a reply?]
And I see no significant advantage to the change in technology itself. Optical ports provide a measurable advantage in sound fidelity over analog, but you haven't seen them eliminate composite or component ports from home receivers, because there are also significant disadvantages in cost and length of optical cables. I don't even follow that there's such gains to be made from switching to lightning...
Which leaves me at the obvious conclusion that this is just a ploy to sell more adapters and reap licensing fees from vendors at the expense of their customer.
And remarks he makes like "Cough up the extra $29 for a new pair" convey exactly the tone that is bothering us all.