... just as Comair (DL Connection) and Atlantic Coast (formerly UA Express) have their own airline codes.

From the horse's mouth: the Bureau of Transportation Statistics at USDOT.

For practical purposes, Express Jet can post its profits, load factors, on time performance, etc. independently of CO. I think the RU code, plus the separate stock market trading under XJT, open the door for Express Jet to break away and become independent, as ACA has recently done.