Ethanol is not inherently bad, but in the US, it is largely produced from corn (maize). By increasing the mandate for blending ethanol in fuel, it will increase the demand for corn. Growing corn comes with its own environmental problems.
It's terrible for your engine/fuel system. Attracts water, increases rust, breaks down faster. It's also less efficient than gas, it takes 1.5 gallons of ethanol to equal the amount of energy in 1 gallon of gasoline.
It is also a solvent that can dissolve parts used in vehicles not designed for ethanol. Automakers complained because it'd cost them something like an extra $100 per vehicle under the hood.
I recall watching an uncle rebuild grandma's carburetor, because her car kept flooding. He shows me part of the original fuel jet and the replacement. The new one has a little synthetic grommet on it, the old one has an empty notch in the same spot. They blamed it on the ethanol.
In Saranac Lake, NY, there are several gas stations that sell unethanolated gasoline. It costs as much as super, despite having lower octane rating. I use it for boats. Some planes can also use it; though most planes using gasoline still use 100 octane (ethanol free) leaded gas.
We have a couple stations in town that sell 'Rec fuel', which has no ethanol. It's popular for use in things like ATV's, dirtbikes, small engines like lawn mowers and snowblower.
Making biofuels from waste is fine, but you can't power but a small fraction of transportation demand with it. So it can't be your sole strategy of reducing transportation emissions.
Most likely what will happens is that those uses that can be electrified will be (cars, city buses, light trucks etc.). Biobased fuels, synthetic fuels, hydrogen and so on will have a role for transportation sectors where electricity is not an option (long range planes, ships, trucks).