Does anyone have an idea why a commercial flight of over 500 miles would not fly above 10,000 ft at anytime during the flight? There was nothing unusual about the weather.
Pressurization failure. Do you have a link to the particular flight?
You’re being unreasonable again, porterjet! Why would someone having a question about a specific flight be expected to give the flight ID? 
Just a roundabout way of saying if you have a question on a specific flight help others help you by giving the flight ID!
Yeah my fault. I guess none of us are on the need to know list.
Perhaps the plane had some minor surface damage and you saw a ferry flight (without passengers) to a location with repair capabilities.
I have seen this happen after minor wing damage and a temporary patch/repair was applied; normal flight characteristics could be altered. When this occurs, altitude and speed limits are both lowered for safety reasons.
Gary
Sorry I did not post the particular flight information earlier.
Live Flight Tracker 
Delta (DL) #5027 01-03-2014 KLGA - KRDU
I was on the flight and was just curious. As we neared the halfway point of the flight, we were told that we had been given a “non-standard route”. At that time we were flying at 6,000 feet according to the pilot.
I spot checked a couple of other flights, one also filed 6000 feet but ended up climbing into the low 20s after passing Washington, another flight filed a much more normal altitude on the 1st but 6000 on the 2nd. I’m guessing weather forced flow control to hold relatively short flights to a lower altitude and a different route than normal to avoid massive enroute delays heading towards RDU/CLT/ATL etc. Later in the flight ATC may, on a case by case basis, be able to let some of the flights climb to a better altitude.
Thank you for the insight. That does make sense.