"The main reason I asked an FA prior to departure if I could move was that I didn't have an entire seat. I had absolutely no allergic reaction until she took them out of the carriers and started letting the cat crawl over her and walk the dog in the aisle (leaving the cat, out of the carrier, on the seat next to me). Even putting allergies aside, this is unsanitary and ridiculous - maybe I should live with pet hair on seats, but I should not have to deal with pet hair in my food (she had them out during snack service). "

It is a requirement (I believe FAA, but could be wrong), that the pets remain in their carriers for the duration of the flight, UNLESS the passenger has a doctor's note that the pet is needed for "emotional support" and then all bets are off. Also, service animals, like seeing eye dogs, of course, do not have to be in a container.