There were different types of cheating going on and the sports were also treated differently in the press.
The NFL painted itself into a corner by allowing the Patriots to cheat. Once they let Spygate go with a wrist slap, they had to keep doubling down on their "greatness". It was a cash cow for the big networks so lips were zipped on the Pats, steroids and the Ray Rice type stuff. Just look at Tyreek Hill this year. The networks say nothing. It's disgusting.
MLB has been reputed to be "dead" for decades. The steroids were just one more nail in the coffin. The TV money wasn't the same for the big networks because of the scheduling structure and the more local nature of broadcasts. This, and the commies trying to promote soccer, made fertile ground for baseball bashing.
Good for MLB for treating the Astros like the Pats should have been treated. And the Pats are still cheating because they understand the lay of the land. Maybe all sports are gradually headed toward the Vince McMahon model.