I think it's the same reason that people like the SNES sound - that famous low-pass filter / gaussian filter that made the SNES soundtracks sound a little 'mushy', for lack of a better term.
Playing through Mother (earthbound zero) this really struck me. The entire game sounds better with the RF audio output. I think the composer was using the famicom for reference, as the american NES was half the world away, and in 1989 the only way in japan was RF.
I like it so much, actually, that I am running the RF output through a VCR to extract the audio signal, and viewing the composite video with the RF audio.
So if it's not too much to ask, I'd like to know other people's opinions. Dig out one of those RCA - to - F-connector things (you know, those things you use to hook up an atari):

and try this out. Use the composite video (or RGB if you're rich), though - the RF video is BAAAD.