My SO and I often travel. Typically, we sit on opposite sides of the plane, not together. That allows each of us to do what we want during the flight. She often watches one movie while I watch another. On very long flights, I usually sleep while she doesn't. Plus, we each like a window seat... others don't bother us when they get up to use the restroom.
Once we get to our destination, we spend enough time together, so it's not important to be together on the flight.