The only uncrated animals allowed in the cabin are service animals. Keep in mind there are service animals used by people by various disabilities, I've heard of people w/ severe epilepsy having service animals to help protect and warn them when a seizure is imminent.

I have also had search and rescue dogs on my flight-even one who was at ground zero.

A couple of weeks ago we had 4 dogs and their handlers who just got back from Afghanistan (Marines). These were bomb sniffing dogs, all rather large german shepards. These guys had misconnected and missed their original flt, so they only had middle seats in E+.

Usually we try to seat service animals at the bulkhead, so needless to say I felt for these guys. I was pleasantly surprised that every pax seated on the aisle in their rows gave up their seat for the marines and the dogs. Apparently, they didn't even have to ask. I tried to buy everyone a drink, but had no takers.

Also, if the person on your flight didn't seem disabled, it's possible that it was a service animal who was being delivered to it's new owner.