Those powder guys killed Sunny Smiles & her dog.
That pissed me off so I go to the prison to extract a little revenge.

So everything I try to loot in the prison is marked in red and when I take said loot I get a message "you have lost karma".
Who did I just lose karma with? The powder guys? The powder guys already hate me. I don't care about losing anything with them.

I just always try to play a 'good' character and don't want bad karma in general.

karma is just a general rating of how good or bad you are, it's seperate of your repuation with the individual factions like the powders.

but stealing is stealing this time around even if it's from an evil charcter or group, as long the item belongs to someone, you'll loose karma for taking it

it's not like FO3 where you only earned bad karma when stealing from good people

but don't sweat your rating getting all spoiled, i've been super evil so far, get bad karma around the clock, and my general screen still says i'm nuetral

Steal from bad people, bad karma
Kill bad people, good karma

It all evens out

This.