So the more I've played this game and explored the story, the more I've been leaning towards that the Institute is really the evil group in the game. First off, you start of the game witnessing one of the few clearly evil characters in the game, Kellogg, killing your SO and taking your child. He's clearly evil, as opposed to just being ambiguously evil, like Elder maxson. The further you go into the story, it's clear that he works for the institute and does their dirty work by killing people or doing whatever they want on the surface. Then, you get to kill him, get his clothes, and his gun. Later on, you can join the Institute, and they basically say "hey, want to take over as Kellogg for us and do a bunch of missions for some sweet xp?" You can pretty much put on his outfit, and just name yourself Kellogg (...just this gave me an idea for a Kellogg playthrough.) You become Kellogg, who the game already established as pure evil, and continue the Institute's evil agenda for them. So now, you're part of the Institute, doing their evil work. Also, the Institute doesn't give you any rewards for completing missions (I'm looking at their radiant quests), unless you ask them. They just make you feel like a jerk having to ask for something, after doing a mission.
Everywhere the Institute has been in the game, has a bunch of dead people. Such as University point, which is a whole group of settlers murdered by the Institute because they had some info. When you go to Fort Hagen, the parking lot entrance has a dead settler, who is most likely killed by the synths before you show up. There are many more examples of the Institute being followed by settlers being killed for no reason.
So the Institute is evil, and you're evil for joining them.