I think this encourages more negativity, especially if there is a house member who breaks a lot of rules. At the moment, if someone in the house does not gain points for their house, at least they are not losing them so it doesn't negatively affect the house - and i don't think players breaking the rules should have anything to do with other players. Having houses only able to gain house points still shows which houses are doing well and it means that houses can work together more positively to try to win the cup.
If points were taken off for rule breaking, there would be a high chance of 'sabotaging', where players resort to another house and break minor rules to lose points for that house. Not only would this be quite unfair, but it could also encourage rule breaking in a way.