I just tried the following route - EWR->DES->SFO on 6/10 and returning on 6/18 via the same route back. The price each way was ~$420 (which included 2 layovers).
I priced out EWR->SFO and United/Continental had a direct flight for $369. Maybe I'm the aberration but I think NYT should have done a few more case studies before publishing their results.