So generally, you feel that when the executive branch exceeds it's power or circumvents checks and balances, that those responsible are prosecuted?

No, just that there is such a concept as "exceeds its power" to the point that when they do, their decisions are not legally valid.

A governor/President cannot go and throw a bunch of journalists in jail. Even if he did, the courts would let them out again.

In a communist dictatorship, there is no power outside the executive.