Are my flatmates being physically inappropriate or is that what guys do? how do i tell them to respect my boundaries?

Set limits: Men engage in horseplay and test limits. If you have not told them that there is behavior that is unacceptable to you, then expect more of the same. You need to speak up for your sake ; theirs. Truth be told, if you are too shy to tell them that something they are doing bothers you, please consider getting with your personal physician for some guidance in assertiveness training.