Are you comparing EWR to JFK? Apparently CO thinks it doesn't need to charge low fares for mid-week trips on EWR-SFO/LAX. These flights are invariably busy, and I suspect that much of the traffic is connecting to / from EWR. The UA p.s. flights are much more O/D focused.

There are always going to be last minute business travelers who can't (or won't) make the trip over to JFK for these flights and take the EWR flights instead - I've had to do it myself a few times at $1,200+.

No dispute that the CO product on these flights is greatly inferior than the UA p.s. product.