Kinda like nuclear is one of the most clean power sources we have, until you put the raw waste into nothing but iron barrels and store them in a salt mine, and then wonder why the underground is becoming radioactive.
Planes can be clean, it’s just a question of using synthesized fuel (edit: as in artificially created fuels, hydrogen-mixes, kerosene replacements, the stuff they use for rocket propellant, that kind of fuels), and not refined fuel (edit: from oil). Of course there are some other problems associated with jet planes, but fuel shouldn’t necessarily be one.