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I went with the institute in fallout 4 and everyone’s making me feel like shit about it. Nobody in the commenwealth trusts the institute, and are very weary about synths roaming around. Is there a way to redeem the institutes reputation and have everyone trust them? I haven’t done any missions yet as the director or the institute, But I don’t want to do missions for them if it means I’m going against what everyone else in the commonwealth seems to want. Also by taking out the railroad and the brotherhood I feel like I cut the story in half.

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    I would recommend simply play through the game at least once before worrying about the ending.
    – Nelson
    Feb 20, 2019 at 11:27
  • I agree with Nelson. Fallout 4 is a vwry big game, and therefore many of choices you can make. Do whatever feels right to you.
    – The Mattbat999
    Feb 20, 2019 at 11:36
  • There is no way to truly side with all the major factions in one playthrough. You actually have to do 4 playthroughs: Institute, BoS, Railroad and Minutemen.
    – Amarth
    Mar 7, 2019 at 19:41

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No, unfortunately you cannot change the general opinion on factions.
A pity, because the Institution would make a hell of an asset to any other organization, not to mention to the common ..wealth.

The main reason for the impossibility of reconciliation is a conflict of interest between almost all of the factions, embodied (in Fallout 4) simplistically and symbolically by the Institute's synths:

  • the Institute creates synths to enforce 'peace' in the Commonwealth, alienating all other people in the process;

  • the Brotherhood wants monopoly over all technology, including the synths;

  • the Railroad wants to free all synths from their puppet masters;

  • the Minutemen want to protect the common people against any danger.

More on the factions here.

So, siding with any of the three antagonist factions - the Brotherhood of Steel, the Railroad, or the Institute - initially lets that faction be more or less tolerated by the other two, up to the decisive moment in which you take a stance against (either of) the other two.
The Minutemen will always remain neutral towards a player in alliance with any of the other three factions, deeming the player capable of knowing how to achieve reasonable peace.

There is a way to let all live together in theoretical harmony, but it's an exploit. See here and here.

Here's a similar discussion on the Steam forums.

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