look, in all my time on fo4 tumblr and on the fo4 subreddit where hatred runs rampant, ive still only seen two valid criticisms of the railroad as a faction. ever.
(im putting aside the whole entire slavery allegory for the purposes of this post)
these two criticisms are:
if you (yes, you. the player) fundamentally disagree with the notion that synths are sentient people, the organization makes no sense and is useless. i cant change your bedrock beliefs on what constitutes a person, so this criticism stands
the mind wipes might border on unethical. the idea is good and well-intentioned, but it kinda sucks in practice. synths can choose not to have the procedure, but the railroad's catastrophizing about what will happen if they dont feels coercive sometimes. i could probably be convinced otherwise, but i think this is a pretty good point
thats it. there are no more. im absolutely open to (and would love, actually) yall trying to change my mind but just know that if your criticisms are:
they're short-sighted; the organization will eventually dissolve because there will be no more synths left to help
they have no plan nor reason to help synths post-institute; the moment the institute explodes, so does the railroad
they're too narrow-minded; they should be helping people too, not just synths
by destroying the institute, they're stopping the production of synths; this nullifies their efforts in saving synths and is even, dare i say, hypocritical
their password being railroad is far too simple and the freedom trail is too easy to follow; theyre just asking for another switchboard
[insert member of the railroad, usually desdemona] is mean; the organization is full of assholes
then ur efforts will be wasted on me. all of these criticisms are bad <3
It should be an in-game thing, if you're walking around the Commonwealth and your marker is putting you directly in the path of something that you will definitely die trying to fight, and Deacon is your companion, he should stop you and offer you an alternative route sneaking through alley ways and sewers.
See the routes he takes to not feel so exposed and also how he's following you around, but somehow getting to the places you're trying to get to before you.
I have only really seen one criticism of this which only tangentially related as it was about Deacon using the word “lynching” to refer to (SPOILERS) his past as a synth bigot. 
I have always wondered why no one really mentions this and I am undecided myself even as an American history major and political science minor. I’m curious on other people’s thoughts so please comment or give your ideas in the tags if you’d like!
I dont get people that are like "but the Railroad only care about synths!!! They could never take care of the commonwealth!!!" cause .... yeah thats quite literally their deal.
Not every faction has to be about creating a new government or whatever - Fallout fans with a hateboner for the Railroad are walking red flags and ohh its very telling how they are pissed that this faction isnt about gaining power over others but helping a disadvantaged minority
and before anyone puts words in my mouth, im not claiming that everyone who dislikes the RR is awful or that this part of Bethesdas writing shouldnt be criticised