This sounds like a troubling problem. I've had many horses over the years, and some would kick, but not that hard or consistently. Its usually an issue of them wanting out or being frustrated by being confined in such a small space and having to stand there. In other words, they are bored and want to move around.
Does she stomp or kick when you have her tied outside for long periods of time? If this is the case I believe she gets impatient with being tied, because she can't go where she wants or do what she wants to do. If this is the case, I'd recommend tying her (to a fence, exterior of the trailer, etc) somewhere where she won't hurt herself from kicking or stomping. A tree might be one of the safest bets since its circular, instead of a long flat object like a fence directly in front of her which she can strike. Leave her tied for a couple of hours at a time, with a hay bag so she at least has something to do, and make sure to keep an eye on her while you do something else (yard work, cleaning the paddock, whatever) so you can make sure she doesn't hurt herself. If she is forced to stand tied she'll eventually get used to it and should stop the behavior. Its just like a big temper tantrum.
Another question is, do you have feed inside the trailer when she is travelling, or just before you head out? If you do have feed in when travelling, do you notice it is gone by the time you arrive at your destination? She could be fine while she is eating because her mind is occupied, but as soon as the food is gone she is bored and impatient to get out to relieve her boredom. A hay bag is always a nice choice because it takes the horse longer to eat it all as they have to pull the hay out a little at a time.
If she still won't discontinue the behavior, then installing rubber siding within the trailer may absorb some of the concussion of her kicking. My trailer has rubber screwed to the walls from the horse's chest down. This came with the trailer as a safety measure for kickers. The shipping boots are a good idea if you are really afraid of her hurting her legs.
You may also have her stand in the trailer when it is stationary for long periods of time, and reprimand her every time she exhibits the behavior, unless its an action caused by fear. If while watching her she seems frightened to be stuck in the trailer for so long (it may be the PROLONGED confinement that frightens her, not the initial confinement), then you should take her in and out, leaving her inside for longer periods of time until she is comfortable with standing quietly.
Hope this helps!