Because the components are less expensive.
Let's look at Makerbot2 for a moment and I'll use the numbers from their website, even though it's more expensive than you can get it for elsewhere:
The printer it's self: $2,799
1KG of material: $48
1KG is enough to make about 10 iphone cases, which work out to $4.80 each.
So, if they sell for $25, that is a $20.20 markup. This would mean that after about 140 cases, everything is pure profit.
So, once this point has been reached, they could easily drop the price by $10-$15 and still make a nice chunk of change.
Perhaps you should purchase a Replicator 2 and have at it...
There are assumptions on your part that aren't correct. The Makerbot branding belongs to Stratsys, one of the largest manufacturers of 3D printers and printing services in the business. They aren't making these on a Replicator 2. The Stratasys machines sell into six figures. These parts aren't being printed on Reprap style machines. These are high end industrial machines. A consumer machine like a Replicator 2 isn't capable of the material range or the speed of an industrial machine.
As others have posted, it's not "pure profit". Such statements show a lack of understanding in how a business, any business including home based business work.
There is software involved in not only the market integration to ebay but in the manufacturing space as well. If one were to download the app, they would see that for the phone case item is customizable by not only adding a name but in also changing the the properties of the edges of the case. There are tools like Autocad 123D but they require a more than passing knowledge of 3D modeling and these products are aimed at people that don't know how or even want to model objects.
Some manufacturing business models sell the finished product at about five times the cost of material. Also custom products are able to fetch a premium markup for the cachet of having something unique (or at least the perception of being unique) or something that is made with input from the end user. In fact it's a fundamental pillar of that business model.
While you are entitled to an opinion, it's not well informed with regards to what it takes to run a successful business or the mechanics and business models used in modern manufacturing.