For the same reason Colbert got cut by CBS execs despite being the highest rated guy on late night. Rupert Murdoch, like most billionaires, is a soulless ghoul that lives just for the money, not friendship or loyalty to anyone.
If a competitive news outlet like the Wall Street Journal got their hands on a breaking scoop on a big time White House scandal, they're gonna break that news before their competitors do.
Keep in mind the Wall Street Journal, despite being another Murdoch owned rag tag paper, is not Fox News or the NY Post. It is to Murdoch what The Washington Post is to Bezos. The magazine was founded in the 19th century. It has a strong reputation and history of jounalism that even Murdoch wants to preserve with a hands-off approach. Hell I give him more credit than Bezos in letting his most reputable asset rock on its own. These are respectable independent writers who want to work for this magazine and want to leave behind a strong legacy in covering politics.
Imagine you gathered solid evidence that the President of the United States was the close associate of a pedophile sex trafficker, only to have your work buried out of vague political interest from the top. You would probably leak the story to another news outlet who would be happy to outdo their competitors and break it. You think a ghoul like Murdoch would pass up a good scandalous story and give it to NBC News ot CNN isntead because he's a Republican? Thats possibly millions of new readers gone.
The media business is all about money over everything. Fox News is only what it is because it corners the viewership of "conservatives" (while also serving Murdochs personal politics). MSNBC is only what it is because it can corner the viewership of "liberals", not because the fat cats who own NBC Universal are leftist revolutionaries. You can turn on Fox News and watch black people being slandered, then you can turn on Fox Soul and see it celebrated. It's all a game for ratings, viewership and money.