Costs should be factored per mile. It really doesn't make sense to compare the costs of someone who travels 8,000 miles a year with someone who travels 15,000 per year.

I concur that some portion of the additional food costs should be included, but gas costs will almost certainly outweigh food costs.

Maintainance costs (per mile) are likely a wash, since car maintainance costs (oil changes and tire replacement) are pretty low, while bicycle tires are far more expensive per mile for the same quality of tire. And the cost of a oil change isn't that different from the costs of replacing chains, cables, sprockets and cassettes, etc...

Like the OP I tend to think that there isn't a lot of difference in cost (on a per mile basis) between the two. I do believe that someone who relies solely on a bicycle will have much less miles traveled per year on average and therefore will spend much less than someone who uses a car instead. I also suspect that locality may have a strong influence on the outcome. For instance a community with short travel distances (ie bike friendly) will almost certainly favor the bicycle since it really takes longer average trips before the car starts to become competitive.