Unfortunately, more than a few refs do little to protect the keeper. Their attitude seems to be that if my daughter is "stupid enough to play goal, she has to be tough enough to take what she gets." The girl that kicked my daughter square in the head should have been red-carded, but didn't even get a yellow. If she could legally play soccer with a combination catcher's mask/NFL helmet on, we'd have her wear it!
Well, keep in mind that as she gets older, the game is going to open up a bit - that's just the nature of the beast. That being said, it seems like there's four video cameras per player at games these days, so if you see something that looks like it's clearly over the line, don't be shy about getting the coach to approach whoever's in charge of officiating for your league.