I think they do this intentionally to maximize their revenue. When the legacy carriers release their peak travel seats (i.e. Christmas week, etc.) there are typically some initial "bargains" to be had. For example, my BOS-STT tickets on AA for this past Christmas were $554 each way in First Class. I booked them 331 days out. A week later the F fare was over $900 one way, and coach was $560 one way.
By the time Jet Blue opens their holiday booking window the fares have crept up significantly on the legacy carriers. Jet Blue can and does premium price at this point since they are in the ballpark of where the legacy carriers have gone with pricing on their remaining seats. A lot of the supply is gone at that point!
So I go through this dilemma every year - do I book the AA first class connection when it goes on sale, or roll the dice that Jet Blue's non-stop will have some reasonably priced seats when they open for booking. For this past Christmas I went with the AA connection, which at least price wise was the right choice since Jet Blue came out with $800 one way fares once EMS was added in. So $554 in AA in first with a connection versus Jet Blue EMS for $800 non-stop. They are no dummies...