If you are not an anarchist or some other form of misguided extremist, then you probably agree with the goal or intentions of the state's IC apparratus even if you find a given mission or action of the IC to be strange when looked at and analyzed out of context.
What I mean to say here is that there is a grand strategy at play, but you may, in your lives and in your careers, encounter a single out-of-context action of such agencies and you will be left feeling their actions were odd, but your feelings on the matter are a result of lacking context and that context is, unfortunately, only disclosed on a need-to-know basis.
So, to those not involved in a goven operation, yes, the agencies will seem to be distorting reality all of the time... Use your brain and ask yourself the motive -- there is definitely a context in all scenarios that explains things pretty well and your elected leaders have signed off on that context after hearing the sales pitch of some analyst turned manager in the agency.
TL;DR have faith in the actions of our nation's clandestine services. They are working to our benefit and their lives are on the line.