It's partly because, in the writer making it so obvious that everything is fundamentally against the bad guys, those factions become the ultimate underdogs. And then, on the other side, these writers tend to lean towards desperately sanitizing their heroes to the point of annoyance/blandness to make sure they hammer it in that they're not the bad guys.
True. But in the most obvious case I've seen is when the author associates the bad guys with values that the author assumes to be universally hated, because said values go against their personal beliefs, but in the end, it ironically endears the villain to the public who might see said values as good.
For example, if you have a libertarian author, he might make the bad guys have a government that's omnipresent, omniscient, and highly efficient, reigning in private enterprise and replacing it with public works programs and the like. But people living under broken countries and banana republics might actually appreciate a government that keeps its eye on things, reigns in the rich, and gets things done, instead of a government that kisses the asses of the rich, while issuing endless empty promises and accomplishing nothing.
Or you can have an irreligious author portray a villain faction as devoutly religious to the point where they'd send good people to die fighting to protect a temple instead of abandoning it and being more "rational" about things. But people who are religious might actually admire such a faction that is willing to fight tooth and nail for what they believe in, instead of abandoning their most cherished beliefs in the face of annihilation.
Meanwhile, the "good guys" they want you to worship aren't as fun as the characters from previous decades, they're the good guys because they support the "current thing", even though in some cases, especially in the case with The Boys, the good guys can be almost as vindictive and ill-tempered as the bad guys. Starlight and her team aren't as fun as say, Sonic the Hedgehog, nor do they exude the kind of moral strength that Captain Kirk or the GI Joes did. So it's kind of getting harder to root for them against Homelander, especially given how colossally incompetent they can be; they had the chance to kill him, but failed anyways.