MFN clauses make it seem like only Apple is getting something. Apple, and other small book stores, heck even the big brick and mortar stores can't compete with or don't want to compete with someone who buys 5 billion of something and then sells them at a loss to steal customers. Apple isn't saying only we get this price, they are saying if X gets this price, we want it to. Whats wrong with that?
What??? A MFN clause, in itself, is not wrong... An agency model, in itself is not wrong.
BUT, if you combine the two.... The agency model make the publisher fix the retail price, the retailer looses control of it and can no longer discount it. That alone is not particularly good for the consumer as it removes competition (or restricts it). But, it leaves the possibility of different retailers negotiating different deals...
Introduce the MFN clause that says "you can't sell to anyone else cheaper than what you sell to me"... All of a sudden, all the prices become the same, and the guy that negotiates this gets the best price in the industry.
So publishers get a higher "street" price for ebooks which they control, and can fix at a level that protects their print business. At the same time Apple kills it's competition's main marketing tool: Price & discounting. And this allows Apple to introduce its iBooks at a higher price point, and not have to fear competitive pressures from anyone.
There's no way this can objectively be interpreted as being a "good" business practice, unless you're Apple or a publisher. Everyone else in that market looses out without being given a chance to compete. The only things left is "my storefront is more attractive than yours"... And customers in every store end up paying more that they did the day before for no obvious reason.
So yes, these clauses were DIRECTLY responsible for price increases. And they weren't an accident.