[terryandrene]

As a general rule, I don't think that you can say one is better than the other. Different carriers have different tariffs, different deadhead pay and means of deadhead payment, differents FSC computaion methods, different accesorial payments and different charge backs for things like TriPak or Qualcomm use.
If all thing were equal, I'd prefer a percentage. If tarrifs increase your compensation will increase with percentage, but not with flat rate. If tarrifs decrease significantly percentage recipients will see a decrease. When a carrier's profit margins fall below an acceptable rate, flat rates will decrease accordingly in the future, as they have in the past.

Your best bet is to find a carrier that meets as many of your expectations as possible. Look at all of the benefits of your chossen carrier, not just the Flat rate or percentage payment. Above all, know your annual cost per mile of operations so you'll be better equipped to make a carrier decision