1. Well, Paladin Danse explains the Brotherhood of Steel consider the Synths to be self-replicating robots and basically are here to destroy them because they foresee Synths pulling the whole Skynet and Matrix thing. They believe Synths are more dangerous than the Atomic Bomb because they are capable of rebelling against their Creators and possess free will--which means that they will exterminate humanity when their numbers exceed humanity.
....
Kind of a leap in logic there but the Brotherhood believes the two races can't coexist and are trying to prevent the Quarian situation.
2. The Railroad is full of Synths, people who are married to Synths, people who are best friends with Synths, and people who just think Synths are indistinguishable from humans. They reject the human/robot distinction. Hence, why the Railroad doesn't have a Gray and Gray Morality view of the Institute. As far as they're concerned, Synths are people and the Institute is Paradise Falls.
Pure unmitigated evil.
Given you can romance a Synth, considering them not people is kind of off.
3. As for the Institute being evil, they also use their robots to engage in Terrorism. There was a smaller version of NCR in the Commowealth called the Commonwealth of Allied Settlements which the Institute used their sleeper agents to destroy. They also kidnap people to engage in experimentation.
Spoiler You know all the Super Mutants running around the Commonwealth?
That's the Institute's doing from experiments with FEV.
Those are where all of the kidnapped people are going (those not used as breeding stock and replacements for their own mutated DNA).