So i just finished the BoS questline, made Hardin the elder, and now the NCR insists on shooting me on sight. Before doing this, i was liked by the NCR, having done more than a few quests for them.
Are they supposed to hate me now? Can't even see my rep with them anymore. Any way of redeeming myself if this is the case?

cheers

Brotherhood T-51b power armour is a faction armour that will piss off the NCR.
Luckily, I have already made a mod for the exact situation, as I had the same problem. (Assuming you are on PC)
http://www.newvegasnexus.com/downloads/file.php?id=35298

Load up a save before encountering hostile NCR.

Take off the faction armour.

If that fails...

Put it on again.
Take it off again..
Put it in a storage place.

Fast travel to a location with NCR to check it works.

I not have you worn any of these caesars legion armour, powder gangers outfits, Khan outfits.
If so do the same with any you've worn.

All right, guess i should have clearified. I'm on PS3, I'm not wearing any faction related armor, I have worn the T-45 one i got at the end, but i do not think that it counts as brotherhood armor. Might have briefly equipped some t-51 or whatever its called, need i go hunting for a new set of it?

By the sounds of it there should still be some around though, try out the backrooms behind the elder the first room on the right should have a set.

If not find a stealth weapon ( silenced ranged or melee / unarmed one ) and kill a paladin for theirs with a sneak crit.

If you repair a piece of armor using faction armor your wearing the disguise isn't properly removed, Equipping and unequipping any suit of faction armor will solve it.

This is what I did, thanks for reminding me. Decided to side with Caesar anyhow though, after having to fight my way through several outposts.