Unburned hydrocarbon products that remain sequestered are not a problem for the atmosphere.  Mircoparticles from plastics are an environmental problem as is plastic trash.
Artificial leaves or other production can take CO2 and directly produce things like ethanol or hydrocarbon chains so petroleum products will no longer be necessary or soon even economical.
Major fuel cell manufacturing plants are being built so with combined battery/fuel cells most transportation needs have means to energy sources with sufficient energy density or specific energy to meet transportation needs. Many already exist so scale up will reduce costs.