If there's one thing I've learned from this thread it's that a surprising amount of people take the Institute's word on Synths. I was of the impression that most people understand the Institute are big dirty liars, the devs had to confirm that yes Shaun is the same Shaun, your biological son- on account of the fact that he basically lies to you about everything else.
I know it's the Institute's perspective since the Brotherhood of Steel really don't have a particularly complicated rationale for their opposition to the Railroad. The Brotherhood hate Synths -> The Brotherhood kills things it hates -> therefore the Brotherhood kill Synths. Maxson even states that Synths have free will, or atleast a close approximation and that's why he's mad at them. Again, no complicated rationale: Man not man, but metal man? Max-Son confused -> being confused make Maxson angry -> things that make Maxson angry get smashed! -> therefore smash thing.
The Institute are the ones who feel it necessary to claim that the Synths don't possess free will or autonomy and that anything which looks like such is just a malfunction. The Brotherhood on the other hand, they react to you taking away a Synth they wanted to use as target practice and setting them free the same way a silver back gorilla would react to you taking away their favourite beach ball. They're not going to try and rationalise it to you, they're just going to charge at you and shake you violently before slamming you into the ground as they screech and beat their chest. If nothing else I appreciate their... Simplicity. A lack of pretention is always refreshing by contrast.