This is a glitch and I just spent an hour finding a way around it, so I know.
I was looking for Thanksgiving flights, wanted the SEA-JFK nonstop, used KVS to find the good fare and the right seats in U buckets. First shot on DL.com with no time restriction shows a only connecting flight (w/4 hour layover) and a higher fare ($70). So I went back and put in 1pm and 7am, the times the nonstops depart. Huh, whaddya know... there are now 4 different options, including the nonstops I wanted and at the substantially reduced price.
I've pretty much given up on Delta, this just isn't a glitch, it's intentional programing, using defaults to drive and take advantage of user behavoir. It's not the first thread on deceptive results on DL.com either...