i have been seeing this alot all over the boards with no one understanding why they are being attacked.
from what i have been reading alot of you have the same problem, you are forgetting about your companions.
if you are friendly or neutral with the legion/NCR/BOS/powder gangers/insert other faction

your choice of a companion can override both your own status with the faction and your "disguise" armor

example if you are friendly/neutral with the Legion
and say your companions are Boone and Rex
Boone Former NCR first ranger will automatically make you hostile to any and all enemies of the NCR as long as you allow him to follow you
where as Rex the RoboDog does not have this affect.

so be aware of which companions you are walking around with so you know who will shoot you on sight