If I had to guess there are probably a bunch of factors in play
1) He came from the Rays, one of the most progerssively-minded, forward-thinking orgs in baseball. So he would've had the expectation of being of that frame of mind. He also probably would've said all the right things during the interview process. Not saying that he intentionally deceived the team, but he likely didn't line up with what the expectation of him was coming in. It seems like the team was pretty heavily set on having a Rays-lineage manager too given that their other significant pursuit was Rocco Baldelli.
2) It seems like the players like him (because he's a good guy by all accounts) and they probably don't want to give him the boot without significant just cause in order to not alienate them.
3) The team has done reasonably well in his tenure. Probably not as good as they should given the talent and the sabotaging efforts of Charlie's decisions, but it's not like they hired him and the team scuffled its way to barely hitting the .500 mark that would make it an easy decision to fire him.
4) There don't seem to be a ton of obvious replacement candidates out there unless you want tired retreads.
I think he does need to go and I hope if the team underachieves again this season it might be a tipping point, but I can see the rationale that might be saving Charlie even if I don't agree with it.