I've got carpet in my car that's about ten years old and that doesn't smell. As for not being hygienic, we hardly ever lay down and lick the carpet in our van and we almost always eat our meals off of plates and to be doubly hygenic we take care to use a table as well.
Each to his own. My van looks and is clean. From the comments so far it would seem that vinyl and rubber are preferred with a temporary piece of carpet on top for bare feet moments.
That's fine, just stay away from carpets and be careful if you're licking windows in sub zero conditions.
If your carpet is going to go mouldy and damp in the winter, that is no place for your bus! In any case you can take it out of the bus in winter and keep it somewhere dry. I have carpets in my house (as most people do) and I don't have any problems with mould, damp or bacteria!
I have a roll of astroturf left over from my grandsons newly carpeted bedroom floor (he loves football), i may try that in my van, well it is green as well!