In my opinion it is what it is.. Personally I was annoyed with naive Starfleet officers like Julian freaking Bashir who want to cling to morality at expense of survival. Bottom line is this, the Federation IS no different than any other race when it comes to survival. If it is between morality and survival, Survival will and should always win. We saw it in In the Pale Moonlight - no Romulans = Federation loss. Saw it in Extreme Measures - Genocidal Founder Killing disease? The Federation was on the verge of collapse. Ransom and his aliens in Equinox.. yes his justification was completely wrong morally, but in the case of survival seemed like the best option at the time.
Bashir said once "so what we are saying is that we are no different than our enemies? That we forget our principles blah blah blah..." Yes, Dr., because if we clung to the rules of war and morality there would BE no Federation. It would have been conquered centuries ago. I am glad DS9 devoted entire episodes to this dynamic because it really irks me personally (I REALLY REALLY dont like Bashir).
The reasons that the aliens don't trust humans is because we are hypocrites and don't always what is right and practice what they preach. It sounds vane, the words had no meaning, when you preach about tolerance, peace and doing no harm, but behind everyone's back you are out doing things like removing a bunch of alien race from a planet in secrecy in order to take over their planet and planted false evidence on some alien politicians to get rid of them because they don't support the idea of making policies that will benefit the Federation. If you believe in your ideal, stick to your gun and people will take your seriously. This is why it is important to stay neutral, not siding with any powers, because then it shows you are serious about not harming anyone and that everyone is entitled to their opinions...that you see everyone as equal and respect everyone's opinion. Respecting people and their opinions is a better way to gain someone's respect and trust. They are less likely to attack you.