Groupings (raiders, synths, arrows) (Fallout 4)

If you destroy these "groupings" will not any faction change to you negatively?
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well, raiders are understandable, ordinary bandits, they will only thank you for killing them.
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But let's say arrows? They are the military, in fact, they are not the first to attack, if you only come as an uninvited guest to their fortifications, they like to build up on bridges, then they begin to beat you. And so if you meet somewhere in the wasteland, they open the fire if you come close to them, and so they keep neutrality.
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well, synths, they immediately attack, but if you destroy them, then the institute will not have any negative (I have not yet reached it) I xs, how is it arranged there.
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Super mutants are still, but they are like raiders. This is understandable
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In general, who can you shoot without fear of losing your reputation?