I noticed that, too.
At first, i thought that the reputation system was somewhat like in GTA 2 - to raise your reputation at the NCR, you might need to kill some Raiders, Enclave soldiers, Thugs, whatever, but...
It seems you can ONLY LOWER your reputation and there is NO WAY to wash you west clean.
Please, tell me that i'm wrong. There must be a way to atone your evil deeds. Dig uranium, kill deathclaws with bare fists, crippling yourself or...
I have a new suggestion now.