History of the fee:
When the dock connector was introduced, third party manufacturers had to pay 1.5% of the RETAIL price of an item as a licensing fee to use the dock connector.
Later, when Apple saw how big the 'dock connector accessory' market was becoming, they upped the license to 10% of the retail price.
Now it's becoming a flat $4.00.
Examples:
1. Cheap: If an item had a $35 retail price, it's fee would have started as $0.525 (52.5¢) per unit. On a retail $35 item, that's not too big a deal. When Apple raised rates, the fee would have increased to $3.50. That becomes noticable. Under the latest plan, the fee increased to $4.00, or ~11.4% of the retail cost. Many cheap items don't even have an 11.4% profit margin. All of a sudden, cheap items become almost untenable to produce. (An item whose retail price is $20 or less becomes essentially impossible.)
2. Expensive: If an item had a $100 retail price, it's fee would have started as $1.50 per unit. Not a big deal at all. When Apple raised rates, the fee would have increased to $10. Not insubstantial, but not horrible either. Under the latest plan, it drops to $4.00, or 4% of retail cost. This makes it better.
Basically, Apple is trying to get rid of 'cheap' accessories, those under $40. (Since that's the point at which the old fee and the new fee are the same.) At the same time, they want to have more expensive accessories; probably for two reasons: 1. It makes the iPod more of an 'upscale' device, since many accessories will be 'upscale'. 2. It locks users into the iPod, having spent possibly more money on accessories than on the iPod itself, when it comes time for a new music player, you'll be inclined to stick with an iPod, even if a competitor is cheaper and better. A corrolary of this is that since you're locked into the iPod, you're also locked into the iTunes Music Store. (Among large 'commodity' stores, anyway. Small niche stores that sell in mp3 are obviously vendor-neutral.)