No, the claim is that they are doing that selectively, along with other things like directing people searching for a book to other publishers books, and extending the shipping time for the targeted publisher's physical books -- as means of discouraging purchases of the targeted publisher's physical books to create leverage on contract terms related to e-books.
Is there something specifically wrong with that sort of leveraging?
Businesses in the online and physical world negotiate all sorts of things selectively for their own benefit. Amazon doesn't give every publisher the same deal just like I'm sure publishers don't give every author the same deal.
There are multiple ways to get books published and multiple ways to sell them.
Amazon is big, and as one of the linked NYT articles says 'controls about a third of the book business', but that is a far cry from the modern-classic example monopoly of Microsoft on the desktop (90% share) in the 90s or perhaps Comcast (Sole option) in some places today.
Amazon and Hachette are doing what big businesses do and authors, who have a direct relationship with Hachette, not Amazon are apparently suffereing.
I'm not seeing how Amazon becomes the villain here.
Better shelf placement, positioning near the front of the store, checkout placement ... All assets that retailers can exploit to woo vendors. Amazon is doing the same thing. Their assets are less tangible but offer just the same incentive to cooperate and play by their rules.
If you don't, you get pushed to the back of the store, placement out of eye level, etc.
The articles don't go into detail, but from what I've seen of the relationship between Amazon and the publishers, I'm inclined to think that Amazon is probably trying to push for very unreasonable terms. Which is to say, Amazon is used to pretty much dictating whatever terms they want to the publishers, because they are in such a dominant position, and I expect that this is just more of the same.