Why is my rabbit angry after cleaning her hutch?

My bunny thumps after I clean his cage also. It just there way of saying stay out of my house but, we have to clean them. Tara will get better at t once she gets used to you cleaning the cage. oh yea i don't put news paper in with mine you know you can litter train her. just get a litter box and put her in it most of them get the hang of it right away and if she doesn't I like to use bedding you can pick it up at wal-mart rather cheap!!Oh yea now when me bunny thumps which is not often I just say (hey knock it off) and he listens lol!!