If Amazon and B&N can still offer more variety of books at a lower price then more power to them. Apple has made no attempts to prevent eBooks from other sources from being read on the iPad.
The problem is the 6 largest publishers got together and decided that they would only use the agency model with a 30% profit for the retailer. End of story or else the retailer can go suck rocks. It's not like 1 or 2 publishers did this independantly. All 6 agreed to the exact same terms at the exact same time when Apple made the exact same agreement with all 6. Amazon didn't have a choice at that point.
If you look at the complaint, the DOJ has plenty of emails and phone conversations that show that they definitely colluded together to do this.
If all else fails, lower your standards.