Am I being unreasonable if I complain about her treatment and get the registration fees refunded?
Totally unreasonable. Your DD hasn't been treated poorly, it's very normal to have more than one goalie on a team, just as it's normal to have subs for any position.
They initially wanted them to spilt each game and we said no as we didnt want to travel to the faraway games or 40 miles for 30 mins playing time and could they do 1 game on and 1 game off
I'm amazed that the coach agreed to this - my DH was a kids football coach for many years, and several of the kids would get only 30 minutes of play each week - otherwise, it wouldn't be fair to the subs, having to travel to a game just to sit on the sidelines, while some children played the full game. If a parent had asked that their child played the whole game or they wouldn't attend, DH would have given them short shrift.
Football is a team game. It's very normal for players to only play part of a game, especially in kids football, where the coach may be trying to give fairly equal game time. If your DD doesn't want to play anymore, that's her choice I suppose, but I would be encouraging her to go along and play, even if she doesn't get a full game. I certainly wouldn't be making a complaint to the club.