Was it a hotel in an anglophone country? Like Jura said, it is a mistake. Foreign hotels are known for massacring languages of all sorts (not just English!). But then again, even native speakers make mistakes in their own language.
Incidentally, in very proper English, "prefer" requires the subjunctive mood, so a hyper-critical grammarian might suggest:
Do you prefer that your roommates not smoke?
Do you prefer that your roommate not smoke? (even when "roommate" is singular)