There are so many of these processes which are so difficult that they border on the outright criminal, but the FTC goes after Amazon because it is a big political target to hit. Maybe from a utilitarian perspective it makes sense.
Bad practices by NYT impact 3% of Americans. Bad practices by Amazon impact 48% of Americans.
You can be cynical and say that going after Amazon is political because more voters are impacted, but at the end of the day it seems reasonable to go after the biggest target where the biggest impact can be made to benefit Americans.