Meh, it may be against the lounge rules, but if the dog is being quiet and staying put then it wouldn't bother me. I'm not a fan of enforcing rules just for the sake of enforcing rules. If this was a small dog sitting quietly on the person's lap then it doesn't make too much of a difference to me if the dog is doing that or in a carrier.
That said, I don't blame the lounge staff for asking the person politely to put the dog back in the carrier either. They're just doing their jobs too.