Long story short, after getting to New Vegas and talking to Mr. House the first time I completely ignored the main questline and went around doing a bunch of sidequests, got liked by the NCR, did the Brotherhood's quests and kept Elder McNamara in power. I really wanted to get power armor like in every other Fallout game so I joined the Brotherhood and figured it was time everyone stopped crying about Caesar. It just so happened right before I joined the Brotherhood one of Caesar's minions invited me to come visit his fortress. I took the boat across and with my trusty Q-35 matter modulator and T-51b Power Armor and wiped out Caesar and his legion.

Loved by almost the entire wasteland after kicking Caesar's ass, I figured I'd go visit my good NCR buddies at Camp McCarran to party it up. As soon as I got there I couldn't even ask the time of day before they were trying to blow my head off with their rifles. Wasn't even wearing Brotherhood faction armor, in fact I tried visiting them completely naked and they still shot me on site.

My question is basically, does being in the Brotherhood make you kill on site to NCR and Crimson Caravan no matter what? Is the only way to hang out with my NCR buddies by wearing their armor?

Brotherhood are enemies of NCR. That is why they are hidden, becuase they lost the battle against NCR at Helios One.

Right, but how would they know I was a member if I wasn't wearing their armor and they live underground where the NCR can't know I joined them. It's not like the brotherhood goes around the wasteland going HEY HOOPLEHEADS, THIS GUY JOINED THE BROTHERHOOD, BETTER SHOOT HIM EVEN THOUGH HE PRETTY MUCH SAVED THE MOJAVE AND HELPED YOU OUT MANY TIMES IN THE PAST.

If you weren't wearing your armor it might have been a compainion bug. Sometimes they just attack people for some reason.

My first game I did the NCR finish as a member of the Brotherhood.

Yeah, I figured it might be bugged, is there a console command I can use to reset my NCR faction standing, but still have them shoot me if I put on Brotherhood specific armor?

You also might have improperly unequipped your power armor. In order to remove the brotherhood disguise you have to (assuming you are wearing it right now) unequip it, exit your inventory (now you are naked) open your inventory back up and equip a neutral or NCR armor. There is a bug in the game that if you simply equip another armor while wearing the faction disguise armor the game will not remove the disguise and you are still labeled as part of the faction whose armor you were wearing. Not saying this is your problem but it is something to check.

The Brotherhood armor makes you disguised as a member of the brotherhood of steel which they are currently enemies of the NCR because of disagreements with Technology. The BOS doesn't want humanity to repeat the mistakes of the past but the NCR care about getting more power and turning that machine into a profit such as hoover dam.