This is a tough question to tease out, because it's tough to define "misconduct." I'd be hard pressed to offer a percentage for how often officers are appropriately punished for clearly violating established law. Because of the code of silence, it obviously happens, but I'm not comfortable saying whether or not it's the norm.
What I will say, based on experience doing civil rights cases and the like, is that I think there are a lot of reasons why anything other than a complete slam dunk is very hard to prosecute against a police officer. And that's in a variety of contexts. Criminal prosecutions, civil litigation, and administrative proceedings.
It's useless to belabor the point on criminal charges. We've made it on the board a lot. Prosecutors generally have a conflict of interest in going after cops who they otherwise rely on. Not just because they rely on a given suspect as a witness in other cases, but because they rely on that suspect's peers. Administrative proceedings within departments present the same problems. And because there are a variety of softer punishments available, there is a real incentive to give what amounts to a slap on the wrist.
In civil litigation, qualified immunity is a huge barrier to individual liability and supervisor and municipal liability is incredibly difficult to prove. In the worst cases, the Justice Department will get involved and the force might have to operate under a consent order supervised by the District Court, but the Feds' appetite for that really depends on administration.
Finally, there's the fact that a lot of what I consider "misconduct" isn't illegal. The use of civil asset forfeiture in this country is a national disgrace. But it's not illegal unless we overturn a host of precedents that allow it for probable cause instead of a more demanding standard.