29 actually isn't too bad for that 6:00am OMA-MKE flight. Here's why:
(1) It is mostly local traffic and very few connections.
It is scheduled to arrive too late to connect to anything except Columbus, Newark and Nashville. (DC too, but there's OMA-DCA nonstop.)
(2) Today's total of 29 likely was only local traffic.
This flight arrived a few hours later than scheduled, so all connections were broken. What connections there were in markets like OMA-EWR were probably rebooked on other airlines in Omaha.
I know this flight had more than 29 people originally booked, but I don't know how many may have been no-shows versus how many were booked on other carriers (like OMA-ORD-CMH) to their final destination.
These point-to-point RJ markets generally don't run load factors nearly as high as mainline. What makes them sink or swim is high enough fare levels coupled with decent local traffic. Connecting traffic fills seats but doesn't bring in the revenue local traffic does.
Here's an illustration to this point.
Six months ago, Skywest shared the local OMA-MKE market with Frontier, and they kept average fares low. There were a lot more connections via MKE, but those connecting fares in markets like OMA-MKE-LGA had to be split between both segments.
Six months ago, a flight booked to 90% (45 pax) might have looked like this:
15 local passengers @ $105 = $1575
30 conx passengers @ $56 = $1680
total revenue........................$3255
I got to $56 for connecting passengers by using an average fare of $140 in markets like OMA-LGA and allocating 40% to the shorter OMA-MKE and 60% to the longer MKE-LGA.
Today there were 29 people onboard this flight, and they were likely locals. Skywest is gone, and fares are somewhat higher. Currently the lowest advance purcase fares are $119-$130 depending on day, with last-minute fares at $231. I'll pick an average of $135 for this illustration.
29 local passengers @ $135 = $3915
total revenue........................$3915
In this illustration, today's flight with only 29 passengers onboard would have brought in 20% more revenue than the same plane with 45 passengers onboard six months ago.