It's probably cleaner than one that's not wrapped in plastic; which of course is not necessarily all that clean.

I don't usually worry about the blankets; if I'm cold, I use one. I'm so not a germaphobe though. My desk at the office is very possibly dirtier than the AA blankets. (Not that I'm a huge slob, but according to research, women's desks tend to be germy because we're apt to have snacks and makeup lying around).