Unfortunately, things that are manageable at home with just a few children, like dealing with spilt squash, become impossible when dealing with 30 at the same time as trying to teach.
Therefore, schools have rules to make things run smoothly that you wouldn’t need to have at home. (Similarly, most parents don't make their children put up their hand before asking a question.) If you don't understand why a rule is in place, then ask. If you don't like the rules, then you are at liberty to move your child to a school whose rules you do like or even remove her from school altogether, so long as you ensure she receives an education.
However, being kicked repeatedly is an issue that you should be approaching the teacher over. Be aware though, you only have half the story. It may be that the child is kicking in response to something your child keeps doing (deliberately or otherwise), or he's not actually kicking but simply doesn't have enough space to sit down without his feet touching her. Or he might be trying to provoke a reaction from her, get her to move so he has more space, create a distraction or, most unlikely scenario, to actually hurt her.
Once you have spoken to the teacher, it should stop. If not, tell your daughter to put up her hand and tell the teacher, and if it still carries on then go back and talk to the teacher again.