I played through as an ally to both. I stuck with the BoS because, well, better toys. But I've spent more time overall doing Minute Men radiant quests, because I like helping the settlers. Doesn't hurt that it's one of the best ways to level up without having to advance the main plot if you don't want to do so. By the time I set out on the last few BoS plot missions I was in the 40s with the X-1 power armor and some cool modded weapons.
Of the four factions (and we're being generous to call the Railroad a full faction), the Minute Men were the closest to an uncorrupted force for good. As for the BoS, they always struck me as absolutists but given the condition of "normal" humanity I can't fault them for seeing the world as "us" versus a whole lot of them. After all, there's no way to play the fame WITHOUT killing a ton of ghouls and super mutants and synths, so the rhetoric is no different from the actions you HAVE to take. Whose more "racist," the person who TALKS a lot about hating these other types of beings, or the person who constantly KILLS those beings?
Where I really started to feel some sort of regret in choosing the BoS was their choice to set off a nuclear explosion under Boston. Innocent people were CLEARLY killed in that blast, and if the blast didn't do it the additional radiation would help to finish the job. Plus there's yet ANOTHER area of Boston reduced to an unusable radioactive pit. The BoS DID have other choices available: just invade the Institute, kill the defenders, and take the facility. There's no reason at all that they couldn't have achieved their goal of ending the Institute's work without detonating a nuke under a populated area. Not to mention, the BoS spends the whole game talking about their mission to find and preserve as much tech as possible. The Institute facility was the jackpot of all jackpots in that department, so nuking it wasn't the smart play for the BoS, not by a long shot.
The game should have let you knock out the Institute as an organization, take the facility, and then start moving your settlers down into a radiation-free, secure environment. Let them see some clean floors for a change.