The standard mark up for any company is 50%. See the article is forgetting a lot of stuff. Here is a brief list of what would go into the phone that Apple will have to pay for
1)iPhone R&D, Yes the R&D budget is not connected, but w/o return future products may not be developed.
2)Employees, Apple had to (and still is ) hire a lot of new employees to work on the phone, this Also includes HR hours spent reviewing resumes and doing interviews.
3)Advertisement,No one would know about the iPhone if Jobs never showed it off.(Fan fare costs money) Websites as well as other advertising they might do after the release, as well as in store displays.
4)Legal Fees, Cisco was not the first to and they will not be the last people to sue Apple. Apple has approx. 15 open lawsuits (one with Apple bundled in as a defendant with the company I work for)
5)Actual cost of parts, What Apple has to pay to get the parts they need.
6)Labor, Apple needs not only R&D, but software engineers, Hardware engineers, direct labor, and QA.
7)Facilities, Apple has to pay for a place to design and make the phone. This means everything from the cost of the building, utilizes, grounds, maintaince, and taxes.
8)Transportation, They have to find a way to get the phone to you.