It seems like the 800 lbs. gorilla that you failed to acknowledge was in the room, is the mitigation of CO2 emissions.  I think this issue is first and foremost on the minds of environmentally minded people, for good reason.  So while your footprint test showed a negligible effect from your transportation use, more than 30% of the CO2 emissions in the world come from transportation.  Call me crazy but if we don't address CO2 emissions sometime soon, that will have just as detrimental effect on biodiversity and the health of rainforests.

Since you cite in your piece that biodiesel is carbon neutral (which is not entirely accurate it's more like 78% fewer CO2 emissions that regular diesel according to the DOE), it seems to me that it's an option worth exploring for transportation.  Again, if the climate changes dramatically due to CO2 emissions, and most think that it will, what affect will that have on arable farm land and the cost of food.

You just can't evaluate new technologies and biofuels in a vacuum.  By that, I mean that you can't judge biodiesel as a fuel based on a model of "if everyone used biodiesel," because that's never going to happen.  Biodiesel is one option to reduce emissions, so are hybrids, so is cellulose ethanol, so is increasing CAFE standards, so is raising the gas tax, so is funding mass transit.  It's not a be-all, end-all option for our transportation needs, no one option ever will be, and it needs to be evaluated as such, the market will decide the rest anyway.

What bugs me is that you seem to ignore the positive aspects of biodiesel.  While you acknowledge the carbon neutrality, it also serves to get people thinking about energy independence, sustainability, and higher efficiency diesel vehicles.  Now, I'm generalizing, but if just 10% of the country started thinking about these issues, instead of more horsepower for their SUVs, that's a good start.  It might actually get people thinking in terms of "biodiversity vs. driving their cars" -- which is an entirely different paradigm than I see in America right now.

10% of our fuel from biodiesel isn't that far-fetched, and its impact on farmland and the cost of food shouldn't be terrible if we can start using better feed crops that soybeans.

If your primary concern is biodiversity, you absolutely must consider the effects of climate change.  And if you are concerned about climate change, you absolutely must consider the most egregious greenhouse gas emitters, motor vehicles.  Biodiesel isn't the only solution, it's no silver bullet, and we can't expect every car to run on it but that does not diminish its benefits.  

You forgot algae bio-d.

Grown in solar cogeneration facilities it can produce many more time the biodiesel per area.  And other byprodcts of solar cogeneration are heat and cooling capacity, waste treatment, clean water, solar electricity, and other biofuels..like methane, methanol, ethanol,and  hydrogen.

This process combined with a major switch to plugin hybrids that only ocasionally burn ANY fuel could actually eliminate imported oil.  The figures DO line up, unlike the estimates of a total biodiesel transportation economy supplied by agri-chem crops.

Good essay, but you write as if all Biodiesel comes from newly planted soy beans.  Biodiesel can be made from recyled restauarant fryer oil. No acreage required.