Eventually, they are going to disband, because as Deacon himself says, they don't care about the other problems the commonwealth faces. With the institute destroyed, and no more Synths being produced, the Railroad is going to run out of Synths to save. After the end of the game, their days are numbered. The Railroad exist for one reason and one reason only: the liberation of Synths from the institute. As soon as the PC and Preston die, the Minutemen are going to disband again, just like they did before. Nowhere is this more apparent than during the quest 'Pinned.' If you fail the speech check, the minutemen you are try to get to stand down will refuse to obey you, despite the fact that you are their leader! 'This isn't the army, we don't have to do what you tell us!' This one line of dialogue makes it painfully clear that the minutemen aren't the foundations of a new NCR, but a loosely organized group of armed farmers that are only held together by a cult of personality, and barely so at that.
The problems that plagued the Minutemen before the player arrives on the scene are still there in the endgame. I know it may sound crazy, but when you think about it all the other factions in the game will lead to tragedy if you side with them.
