my coop is raised off of the ground so there's area to hide under there. What they end up doing is flying to the top of the coop to get away from the hens.
So they're not really able to use that space to hide then. You need more clutter from the sounds of it?
Right now I have 4-wk-old chicks out with hens, and one of the hens really likes gunning for the chicks. My layout looks something like this (not up to date, but close enough):

Every obstacle has at least 2 ways out. If the hen chases one way, the chicks run another. If the hen gets up on something, the chicks fly down. Past the first day or so I don't interfere... the chicks need to learn to run for it, and they figure out pretty fast what the best safe spots are.
I also have 4 food bowls out in the morning so cranky hen can't chase off the chicks forever.