A.D.
Depending on what time the bus is, there may be really bright morning sunlight, this could be causing her headaches. You can ask her if it's bright and sunny on the bus, if she says yes, you could get her some sunglasses or a hat with a brim (sometimes you can wear a baseball cap under a warm winter hat so she can still stay warm). This is possibly an easy fix. Otherwise, I don't know what on the bus could cause headaches - too much noise maybe? Good luck.