I've been reading that part of the main story is siding with one of the four factions. Without being too spoilery, is this completely true? Or can I for example ally with both the Brotherhood and the Minutemen, and rescue synth Shaun?

yes its true.. with 1 change.. the minutemen are a neutral faction and the only outcome with any problems with the minutemen is the institute path but you can talk your way out of being enemies with a charisma check... all other factions are ok with you being part of the minutemen and minutemen can put up with institute if your persuasive enough.

oh that good because im thinking of just killing the instiute the moment i enter and then going back and murding the railroad while leaving the minute men and brotherhood alive

Is there any sort of overarching questline for the Minutemen? It just seems to be helping settlements out rather than being the big hero, which is a refreshing change. Do they conflict with the Brotherhood at all? Do the Minutemen ever play a part in obliterating the Institute?

1. Not really. The settlement helping IS their MQ. Of course, once you do enough, you can get the Castle as a settlement.

2. The Brotherhood has no problem with the Minuteman. However, if you did the Minuteman ending and made the BOS hostile, you can wipe them out with artillery.

3. Yes, the Minutemen can destroy the Institute.

You sorta put a major spoiler at the end man.