The biggest thing for me is past experiences and the known conditions of an airline's fleet. If I've had to go through some strange and negative experience on an airline, I will never fly them again. Same goes for if they have a much older fleet (à la Delta). I just don't trust the older birds as much and they're not nearly as comfortable.
Meals are also very important. Considering the fact that nowadays they're really limiting what you can bring on planes, they better have a meal or two because being hungry on a flight for me is nigh to torture. I tend to choose BA whenever I go to the UK because I like their in-flight meals.
A loyalty program is just icing on the cake for me. ^