So after considering carefully I finished the main quest with the Minutemen because - in my opinion - the Railroad is just too small and too freaky, the Brotherhood is too militaristic and the Institute is the killer of mankind.
I killed Father the moment he revealed to be my son, because my character couldn't and wouldn't believe him
I then did several quests for the Brotherhood, the Minutemen and the Railroad. I wasn't able to finish MQ with the Railroad cause I had killed father but the Brotherhood would still have been possible. Nevertheless, I went with the Minutemen.
The funny thing is: Even though I did that, I'm still on good terms with the Railroad AND the Brotherhood. I can do side quests for both of them + the Minutemen. Deacon and Danse (whose life was spared because I demanded it) are still my companions. I've only missed the Institute companion XYZ (or what his name was...)
This was not intended and I didn't think it was possible. But I guess I can live with that.
I though when you go the Minutemen line you would be enemies with the Brotherhood?!