A bit of background: My son was very active in high school wrestling. However, the coach--basically a "good guy" who really thought he was doing the best for the team and the wrestlers--treated my son very unfairly. He had his personal favorites and his own biases, and these inevitably came out. So I've definitely been where it sounds like you are.
The first thing to do is for your daughter to talk to the coach. Maybe she's already done that. But coaches expect to hear from the player, not the parent...as difficult as that may be for us as parents. Coaches want kids whose top priority is the team. (Some do acknowledge that performance in school is also important, but assuming academic performance is satisfactory, dedication to the team must be absolute.) So the player must go to all practices (varsity wrestlers at my son's school had practices through the winter break...including New Year's Day). They can't be seen as slackers. Attitude is critically important. And if the coach decides to put someone else in, when the athlete (and his/her parents) feel that that's unfair, you just have to smile and go on.
Also, as a parent, make yourself valuable. Volunteer to staff the fund-raising snack bar during athletic events. Help out in other ways.
OK. If that doesn't work, schools have a structure, a hierarchy. There's an athletic director above the coaches. However, in most cases the athletic director will not get involved. They give the coach almost total autonomy. You can appeal to the athletic director, but odds are the athletic director will respond that it's the coach's decision. And going above the coach won't win any brownie points with the coach.
We eventually realized that the wrestling coach just didn't "get it." Our son's problem was a health problem, and the coach just thought our son was a slacker. (Twelve months ago, our son was so weak that he couldn't walk. He'd been lent a walker by a physical therapist who was treating him for a 40% vestibular loss in one ear...and that was the least of his physical problems. He was too weak to use the walker.) But our son "looked" OK to the coach. And you may be encountering something similar.
What we did was find other outlets for our son...other ways for him to excel. In his case, there are pre-season and post-season tournaments. He competed in them and did well. Depending on the sport your daughter's in, there may be opportunities to participate in the same sport outside of school. Our son also took up a similar sport--grappling/Brazilian jiu jitsu. He's now winning regional tournaments and beating other kids who were state level wrestlers. Maybe there are related sports your daughter can participate in.
There are a lot of life lessons kids can learn by going through what my son and your daughter are going through. Some are positive. Some are negative. The overall effect, however, can be positive if handled right. For example, here's how he did recently: http://www.youtube.com/watch?v=3S6oOBw3Trc
Kids are resilient. Support them. Help them. And recognize that there are multiple paths to success.
Hope that helps.