You can join all four factions.
You only become enemies with them if you don't join them all before journeying to the Institute.
One odd thing is the other factions encourage you to join and sabotage the other factions.
At some point in the game you will be asked to help retake a certin area for the Minutemen. It's a big deal so you cant miss it. After that point you will be asked to lead the Minutemen, you have the option to say no.
Just like in real life, they may consider you part of the minutemen already, but that doesnt mean you are.
If you join the minute men it doesn't affect the rest of your quest line at all.