You are never, not ever, out of line to ask your child's teacher questions about the way she or he runs a classroom with your child in it. The teacher should take your concern seriously and give you an honest and professional answer that satisfies you, and if that doesn't happen, she should know that you will take the matter up the chain of command. Ask the school social worker or the principal. Most districts have some kind of discipline policy that teachers are expected to use as a guideline for setting up classroom rules.
Both my daughter's kindergarten and first grade classrooms, the children and teacher had a class discussion on the first day and "wrote" the rules together... both classrooms also used a simple reward system where if a child had no problems for the day, that child would get a sticker to take home and after a certain number of stickers, would get to choose a prize out of a grab bag. My daughter is pretty sensitive but she never got upset about not getting a sticker, I think because it made sense to her when she didn't... there is a real turning point around this age in terms of fair/unfair and wanting to see consequences for both good and bad acts. I think it is this development that makes teachers use physical aids like stickers and cards to teach discipline, which makes sense to me, but in my opinion what you've described is not the best use of classroom energy. I don't even know if all the kindergarteners would be able to keep 3 different sets of negative behavior/consequence sorted out.
In first grade, there was a 3-strikes type system, with different consequences for first, second, and third problems in one day. That would make a little more sense. But in that system, any kind of note home was strike 3-- 1 and 2 were dealt with totally within the school. If a 5 or 6 year old has ONE disciplinary issue on ONE day, why send a card home about it? That says to me that the teacher may have issues controlling the classroom and/or understanding and having patience teaching such young kids how to act in the classroom.