"Commuting costs" are not deductible.
The expenses of commuting to and from work (or to and from school) such as gas, tolls, bus fare, train fare, taxis, Uber rides, parking, etc. are not deductible on your Federal return.
By using a payroll deduction, your employer was either able to purchase Charlie cards for its employees at a discounted price and/or use pre-tax dollars to purchase them. Check Box 12 of your W-2 to see if there was a pre-tax deduction for the cards.