Almost everyone in the Commonwealth fears the Institute, and the Brotherhood is like an invader from outside. I think that's why they gives a decrease in happiness (while the local force of the Minutemen increase it).
That is a good argument for it. It is really just an opinion, with both sides having valid points. For me, it just seems like any settlers that unhappy with those factions would have left when the player begins to ally the Minuteman with those factions. Thus leaving settlers either neutral or happy with the building.
Edit add: Your argument could be used for adding negative happiness for the railroad and Minuteman as well. Not everyone is happy with a faction helping synths. Also negative if the Minuteman is allying with a faction they don't like.
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