That's conspiracy thinking. The NYT covers a lot of negative stuff about a lot of prominent companies because it's interesting to readers. You haven't even demonstrated that Amazon gets coverage out of proportion to its scale [1], let alone that it's unduly negative. And if you did, you still wouldn't have any evidence that it's part of some sort of high-level conspiracy.

[1] Which is huge; they're #5 on the Fortune 500 and employ 647,000 people: https://fortune.com/fortune500/2019/amazon-com