It's not necessarily that the Railroad are good, as much as they're less evil. They want to help, whether or not they're doing it the right way is less sure.

The Institute on the other hand has ostensibly written off the surface, and yet, they continue to kidnap and replace people with Synth's, causing the population to continue to hate and fear them and ultimately leading to their own demise.

The thing about Broken Mask and Coursers, is that the Commonwealth has no examples of good Synth's, outside of Nick. So they are rightfully wary of what they perceive to be the monsters in the dark. Add in University Point, and you have an absolute case for fear.

The Institute bill themselves as Humanities last, best hope, but only the parts of humanity that serve their interests. Add in the fact that they kept releasing Super Mutants into the wild long after learning they couldn't not make them.