Humans aren't "the good guys" in 40K, just like humans aren't "the good guys" in Starship Trooper.
Walter White was a piece of shit.
The cops on the Shield are pieces of shit.
Tony Soprano was a piece of shit.
House was a piece of shit.
Tyler Durden was a piece of shit.
Jim from the office was a piece of shit.
Someone being the main character doesn't make them a good person. Sometimes a story is told from a different perspective, in order to see something new in a darker light.
That being said, there is definitely an issue with people not quite getting the point, and attracting or encouraging the wrong crowd.
I remember a few times choosing to stop playing some people, because halfway through I would pay a little more attention to the glimpses of a tattoo, the patches on their battle foam cases, or what they have up in their garage.