Is that your educated guess? or you have proof?
It's something of an open secret in the industry, and has been alluded to by various industry higher-ups in various articles and interviews. I don't have anything to hand here, and I don't have time to search, so you'll have to take that for what it is.
That said:
How do we know this is not because Apple want too large of the fractions of the $$$ from the sales, and holding users hostage?
The impression given out is always that it wasn't really about profit percentage (more anon), but about pricing structure. In the same way the Apple fell out with Universal about flexible pricing, the majors wanted the option to sell music at tiered prices, with newer songs being more than 99c for some period of time. I believe some labels also disliked the cherry picking of songs from albums and wanted to be able to sell songs at different prices within albums.
Either way, as has been well documented, Apple were pretty determined to keep the 99c price fixed, and they had the clout to make that happen. That made them enemies.
As for sales percentages, a few thoughts:
Firstly, rumour has it (given that no-one really knows) that Amazon is paying a higher percentage to the labels than Apple. However, given that Amazon is also selling for less, it may well be that in pure dollar terms both companies are paying the same sum to labels, and Apple is just marking the price up a little higher. So it might really not be the case the labels have a sweeter deal with Amazon.
Secondly, the advantage of being the dominant player is always that you get better deals than the lower volume sellers. WalMart's entire business model runs on this. If Apple weren't able to get songs for cheaper than Amazon, given that Amazon was way behind in sales volume when the MP3 store was launched, something would be very wrong. Oh, wait, Apple didn't get as a good a deal as Amazon, since Amazon have DRM free from all of the majors, so something *is* a little wrong...
Apple is notorious for its greedy behavior in cutting into partner's profit.
Proof?
Not especially. They played a better game of poker than the majors, and I respect that at a business level. As a consumer, I don't feel better for it though. For all Steve likes to talk about a DRM free world, and how his hands are tied, the labels shot themselves in the foot by mandating DRM, as it gave Apple exactly the kind of lock-in it needed to build some serious momentum.