Commuting costs by car vs. train?

grepdisc writes: Newspapers in Boston are fawning over a report by the American Public Transportation Association that taking public transportation saves money over driving. How can one possibly save $12,600 per year, when the inflated estimates of 15,000 miles per year at only 23.4 miles and $2.039 per gallon costs only $1,310, and a high parking rate of $460 per month results in under $5600. Is the discrepancy made up of tolls, repairs, the cost of buying a car and ignoring train station parking fees?