The Krispy Kreme near me has coffee for a nickel, so I've been going donut crazy lately. First time back to the shop with a dozen, the bungee did dig in to the box a bit and mildly injure some donuts. So I cut a plank of thin plywood the size of the donut box, brought it with me the next morning and laid it atop the box before strapping it to the trailer. Worked like a charm.

If you're using a rack, you could cut two plywood pieces, affix one to the rack with a couple nut and bolt sets and use the other sheet for atop the donut boxes.