I know that Faction Armor sets your rep with the corresponding faction to neutral but I hate it how I bust my butt off to help the Legion/NCR and I don't even get to be a member. Sure, I could always just put faction armor on but it resets my rep to neutral until I take it off so it kinda urks me that I can't be a black ranger :<

I think that it should only reset the rep to neutral if your rep with them is anything below neutral, cause I can only see it being useful to have in that situation.

But I was also wondering that let's say I wear faction armor, and I get some rep. If I were to be wearing that armor while gaining the rep, will could I be accepted whilst wearing it? If not, does the rep still enhance my "title"? (ie. Liked, Idolized, Troublemaker).

Why would I want to wear the armor? With faction armor you're treated like Generic Soldier Guy A. Without you're getting your butt kissed more than Kimball in a room of NCR supporters.

yep, if you wear black armour from the start of the game you'll still gain Ncr fame while wearing it. If you take it off and put it back on though it will be neutral (but not while you have it off)