At the end of the day, the question has to be "Is the publisher getting a better or worse return?"
This is not the only question to ask. I am really surprised at Americans (I am not sure you are, but I see this argument a lot) who say 'well if you dont like apple/amazon/evil-megacrop restricting what content they are distributing you can always get it some other way, it's not like they have a monopoly'. In fact, they DO have a monopoly and I am going to explain why:
A monopoly is when you have 100 % control of the market. While amazon do not control all electronic distribution. They do control the distribution to all Kindles. Basically you can take everybody who owns a kindle and consider them a separate market. And this market they control. To a 100 %. This is the same thing apple does, google and everybody else wants to do this.
This is really the new black. Do not be a monopoly. Create a market (for e.g. stupid apps). Do not conquer the whole market because then you will be regulated. When someone complains about you locking up your market you can always say they can go buy a nokia or whatever.
I think it is really important to realize that these companies are trying to create monopolies that do not look like traditional monopolies. This is no conspiration theory. It's just nobody likes the free market and if you want it free, it must be regulated.