In Skyrim, I could NEVER bring myself to join the Dark Brotherhood. I had no aversion to terminating people that "need killing" like bandits and Thalmor. But the very thought of killing someone for absolutely no other reason than because someone paid me to end the target's life makes my skin crawl. Similarly, after ONE foray into the Thieves' Guild, I couldn't stand ever joining them again, ever. The idea of taking from others just because they have what I want made me feel no better than a common bandit.
So here we are in FO4. Each faction has its pluses and minuses. I have yet to complete the Main Quest, despite having sunk over 400 hours into the game, but I have formed some opinions about each of the factions.
Brotherhood of Steel
Its members are more than happy to tell you if you give them the chance, "If you're not Brotherhood, you're nothing!" That pretty much says it all: They're not prejudiced; they hate everyone. Joining them feels like joining the KKK.
The Institute
To my mind, worse than the Dark Brotherhood. Patently, they don't give a whistle for the lives of anyone that isn't an Institute citizen. What makes them worse is they have no compunction whatsoever about snuffing out non-Institute lives in the name of Science -- no matter how trivial the experiment may be in the scheme of things. It may be argued that it is only The Powers That Be that are doing all the experimenting, but they are TPTB that all of the other Institute citizens allow to be TPTB. Willful ignorance of acts purportedly done on their behalf is no excuse.
The Minutemen
To my mind, these are the ONLY faction worth joining. But as a group essentially led by Preston Garvey, they are so needy, clingy, helpless, and hopeless unless YOU, personally, take care of their EVERY need, on demand, right NOW! that they pretty much alienate EVERY player sooner or later. Noble cause; poor execution.
The Railroad
Freeing any sentient entity, whether it be human or human-made, from slavery is to my mind a noble occupation. But how it is done is just as important as why it is done. The members of the RR seem to think that any non-synth that gets killed "for the cause", either as collateral damage or as slaver scum working for the Institute, knowingly or not, constitute "no great loss". And I have no doubt whatsoever that their attitude towards paranoia-driven Commonwealth citizens is that they are just as "evil" as anyone in the Institute. As such, it seems that the RR has elevated synths to be more important than any other kind of species in the Commonwealth. That makes the RR pretty much just as racist as anyone in the Institute is racist.
If I had my way, I wouldn't join any of the factions. In fact, that is pretty much what I have been doing with my current character of the last 250+ hours. It's quite a bummer that Bethesda has set things up so that it is thoroughly impossible to complete the Main Quest without joining at least one faction. So, given that limitation, I plan to complete as much of the game as possible before finally joining the Minutemen, complete the Main Quest, and then quite the Minutemen at the earliest opportunity. ("No, Preston. I do NOT want to be your [censored] General!")