If all of the additional fuel taxes were used to fund mass transit systems in the area where the taxes were collected, I would be in favor of a tax increase.
I believe the best way to do that would be to have a government mandated tax imposed upon individual cities. If I buy my gas in Cedar Rapids, The money goes to the cities bus system. If I buy my gas in Fairfax, which doesn't have a mass transit system, there should be no additional tax on it. The busses would also have to operate 24 hours a day (but with a decreased number of stops and busses), as many younger people have jobs that start after school and end close to midnight (maybe busses in large cities do operate 24/7, but here they stop around 9, I think).
The families with complex commuting schedules is a very good point. There is really no easy answer for that, because a tax exempt system would need many employees to evaluate whether exemption should be awarded. I think the best answer would be carpooling. It's been around for awhile, and is not perfect, but it helps a lot.