Are you flying exactly 2 aircraft on this route? If so, I believe that it is a bug. I have found that if I start a route with 2 aircraft at the same real time (in other words, within the same game day), both planes will always have appalling yield (~30%). What's more, they stay at that level, seemingly never to improve.
However, if one of the flights is canceled, whether manually be scheduling or automatically by a flight cancellation, the yields will start to normalized. Furthermore, if in the beginning you start the route with the 2 planes on different game days, one after the other, then yields will be normal.
I first experienced this bug when sami changed the yield calculations in the beginning stages of ATB. I reported it, but it seemingly hasn't been fixed. I experienced it again the other day on one of my transatlantic flights.