They have a formula to figure out of the lager object will waive the shipping fee for the second smaller object. It has to do with newegg's shipping methods (giving sufficient space/packaging material etc). No details are released however as to exactly how it works.
In all honestly I wish they would give free shipping on items even when bundled with any smaller item. But at the same time you must realize that free shipping is a costly demeanor, whether having to deal with the source of the products or having to take on the cost themselves. Staying in business while satisfying the american consumer is tough :P
Yea I totally understand the shipping part. I used to work in E-Commerce and shipping is a very expensive thing to be giving away. Both shipping and handling. Handling is killer because those printed boxes they use aren't free and they have to pay people to package etc etc so I understand.
I'm just concerned about their customer service training though. I'm sure the customer service rep I was speaking to wasn't trying to be cheap. She probably wasn't trained sufficiently to handle the situation that came up. Personally if I were the manager there I would train them all to handle these "Free shipping requests" on a case by case basis. If it seems like a good idea to satisfy the customer and make the sale, do it. If it's not worth it, then don't.