"That is, the CO2 emissions from ethanol are not a problem because they are matched by an identical amount of CO2 capture."

You're missing every other machine using non-ethanol fuel to operate which is required for harvesting/producing ethanol biofuel.

Ethanol's net CO2 output is positive, not negative. That is not good.

That would imply that producing ethanol requires more fuel than it produces, so producing ethanol costs more money (for fuel) than the resulting fuel can be sold for - which is simply not true.

While you might argue that some cases of bioethanol in the first world are essentially just farm subsidies, producing sugarcane ethanol in favorable conditions (e.g. Brazil) definitely is profitable in the financial sense and also in the CO2 sense because it saves most of CO2 emissions compared to the fossil fuels they replace.

Of course, even in ideal conditions any fuel has zero net emissions and can't possibly have a net negative CO2 contribution by itself (that would require carbon sequestration) but every liter of gasoline/diesel that gets replaced by a low-CO2 fuel means a reduction of CO2 emissions.

You shouldn't compare something against a fictional zero, you compare it against realistic alternatives, so CO2 emissions are not only acceptable but actually desirable if they replace much larger CO2 emissions.

Setting aside that these are not the CO2 emissions from "burning ethanol", do any of these "machines required for harvesting/producing ethanol" require a "non-ethanol fuel", or do they use that fuel for now just because it's convenient, and could be easily replaced by other sources? I know that the power for the refining plants is produced by burning the remainder of the sugar cane plant (which produces so much power that the refining plants sell the remainder electricity), but I don't know which fuel the trucks and tractors currently use.

Tractors and trucks currently use diesel, but you could convert them to ethanol if required. Most likely existing ones would just be gradually phased out, and new machines would just run on ethanol.

"Setting aside that these are not the CO2 emissions from "burning ethanol", do any of these "machines required for harvesting/producing ethanol" require a "non-ethanol fuel", or do they use that fuel for now just because it's convenient."

You can't set that aside. Consider the whole chain of production and usage or be consigned to a disingenuous selective argument upon the level of quack doctors. Plain and simple.

I'm primary talking about methanol, ethanol is not really as good a fuel and producing it by using biomass is not very efficient. So generally I would be against it but cars should still be able to use it.