What are the benefits of pre-ordering the iphone 6 directly from Apple, as opposed to from a cell phone company (AT

None, really. If you order one with a specific service provider it is essentially the same as going to that provider's local store. However, it's possible a local Apple Store may have inventory before the provider's local stores.

Really none if you are getting an iPhone locked to a carrier...other than Apple typically sets up delivery so it arrives at your door the day of release in the stores.