If we can use electricity to turn atmospheric CO2 back into jet fuel it could still be net zero emissions. At that point the planes are just using hydrocarbons as a means of dense energy storage.
One could already see maybe small scale operations capturing niches - maybe if a corporation that operates a private jet wants to further a reduction in their carbon footprint.
Instead, I'm for transferring funding decisions under the program to a much more open set of actors to originate investment loans (much like mortgage brokers). The investment performances are evaluated on their successes/feasibility, the loans purchased from their originators with high feasibility (i.e. we're scaling known limits), as well as opening up higher origination limits (if they prove out better carbon negative/netural tech). It's more of a financial tooling solution than a tech centered solution. This increases the possibility of failures, but provides a regulated scale out needed with a optimization criteria to keep scaling along successful lines with more organizations rewarded who make successful carbon investments. Experts like ARPA-E could definitely be involved in assessment, but the scale would be completely different then what has gone on before.