I'm wearing Reinforced Combat armour MK 2. Not faction armour
What about your head? I had the Monorail guards randomly attack me in McCarran the first time I was there. I took off the Fiend Helmet I was wearing (I was wearing Wasteland clothes otherwise) and they didn't do it the next time. Could have been a glitch, there are plenty of them, but it could have been the hat too.
If you deal with Yes Man and follow his suggestions, the NCR will stop supporting you... the game warns you of this. Did you agree to do what yes man suggests?
I've had a similar glitch when I've been traveling with ED-E; it was an NCR base, though not the Hoover Dam. My only option was to reload (he also set people off in a drug den somewhere once too, although maybe they were just tweaking and paranoid, who knows).
Actually, if you were there during the president's visit, the NCR will attack you regardless of your reputation if you step into the wrong places, like the stage or back of the Visitor Center.