It's bad that he didn't get any kind of feedback from Apple as to why... however this headline could also read "iPhone Developer Spends $600K Despite Having No Guarantees of Acceptance into Proprietary Platform" ...
The only thing you could really assign as Apple costing you for a delay, is the amount of money you would have made on your app during the time before you ultimately got accepted.
Whether you spent $600k or a weekend building it has nothing to do with apple costing you a dime.
The article should read Company Spends $600,000 Developing App for Proprietary Service that Violates TOS (but Gets No Response).
The article states "FreedomVoice was planning to charge a monthly rate of $5 for the service." This is a clear violation of the App Store TOS (although that will change once 3.0 comes out).
Then, it's simple. Reject the app. Say it violates TOS. Have a nice day.
I'm starting to think that the best way to do a big application is to start small and keep getting bigger. I haven't heard these horror stories of review problems once an application is launched. As it stands, I wouldn't attempt a large application on the system.