What bugs me is that no one in the games explains probably why Synths are dangerous and that makes it look like the BoS hated them for no reason.

What if one Synth decided that Synths should rule the world and enslave humanity? -we kinda destroyed the world- He then reprograms other Synths so they fight for him. Everyone would be against this Synth faction, so even if you sided against Railrod and BoS, the Institute would still help you. And it could even be a reference to the the Mutant Army and the Master from the first Fallout, trying to recreate the feeling and the atmosphere.

Maybe at the end the Sole Survivor either helps the Institute to regains control over these Synths or he unleashes a digital Virus that damages the hardware of Synths in a way that prevents them from being reprogrammed. Or you side with them and become a cool Cyborg.

C'mon would that be totally cool?

The BoS consider Synths dangerous for the EXACT reason everyone else does in the wasteland. They can look like and replace ANYONE you know, and you will have no idea. They are also generally controlled by a group that uses them for not only that purpose, but also for kidnapping, and fighing, and as they are almost limitless machines that can take a beating a normal person likely cannot....well.....yeah. Even after the institute was ruined, Many synths still fight for their cause, so clearly at least some agreed with them to some extent.

Kind of like the changelings/dominion in Star Trek DS9... if you have the ability to mimic anyone, no good can come from it given human nature as it is. It's unfortunate that it only take a few bad apples to spoil a whole bunch though.

But the game never emphasizes that. It looks like the BoS wants to destroy, because they project their hate on them and not because they are a real danger. For Preston everything is just roses and sunshine and he gets away with it. He never has to make hard decisions, he tells the player to order an evacuation before they destroy the institute, but the game never points out that, that greatly increases the risk that the institute will takes revenge.

And beside a Synths are army would be pretty cool.