If you want me to care about the protagonist of your fiction, you need to make him a heroic protagonist. He does not have to be perfect, and he can be flawed. But just as it is easy to make a villain an irredeemable monster twirling his Snidely Whiplash mustache while stepping on a box of kittens, it is easy to make your hero into a square jawed, virtuous and pure all-American hero who always does the right thing all the time. That is why it often goes too far into the other direction – but you do need to have a good protagonist.
This does not mean characters must be Lawful Good Paladins. They can have flaws, and they can do bad things. In fact, one way to make a character interesting is to have him overcome his flaws, or get past his sins and redeem himself. In some cases, he might even have a sad ending to his story because his past comes back to haunt him, but he takes it honorably because he knows he deserves it.
Characters can do morally questionable things, especially in a dark, apocalyptic or chaotic setting. There is a line, though, that characters cannot cross. Once they cross that line, they are no longer a protagonist the audience can support. Making the villain even worse than that “hero” does not make it easier to watch when you have a bad guy fighting a bad guy. It needs to be clear that your protagonist (or your group of protagonists) are good guys, even if they are flawed. Having a couple characters who are more committed to doing the right thing helps too, because they can bring the darker characters back from the brink.
Basically, for me to care about where your story goes and how it ends, I need to care about the protagonists. I cannot do that if everyone is a bad guy.