I'd only be comfortable with taxing carbon emissions from flights if all of the tax money was directly funneled into clean energy research and development. Otherwise, it's just going into the pockets of politicians and funding defense contractors.

No, it's still better for it to be taxed than not. I would be perfectly happy to see a revenue neutral carbon tax. What the tax is spent on is orthogonal.

No, what the tax is spent on is extremely important. For instance, if revenue from a carbon tax is funneled into subsidies for cattle ranchers, it's kind of counter-intuitive isn't it?

Money is fungible. Generally speaking, new taxes are not causally linked to spending on any particular issue.

Obviously, subsidies to cattle ranchers are bad. But whether they are funded from increased debt or a carbon tax does not affect their badness.

The other alternative is to use the tax income to offset other taxes, or even return it directly to citizens as a dividend.

Then what's the point of the tax? I can see how airlines may funnel some effort into R&D to reduce carbon emissions, but only to the point where it becomes profitable to them. Returning the tax as a dividend to the consumer is just as pointless as the consumer is in no way obligated to be climate conscious with their capital.

The point is to discourage carbon-profligate behavior by making that behavior more expensive. If you increased cigarette taxes and used it to lower other sales taxes that would still reduce cigarette use[1]. Maybe you'd get even faster reductions in smoking if the cigarette taxes were all earmarked for R&D on ways to end addiction, but making something more expensive tends to reduce consumption of it regardless of how the tax is later spent.

If you're wondering "why not use targeted legislative mandates instead of carbon taxes?", I'd say that taxes have an advantage in that they're harder to game and need fewer adjustments over time. For example, if you introduce a mandate to make cars more fuel efficient, manufacturers will tweak the vehicles they sell so they are no longer "cars" but some legislatively distinct class of vehicle, and people who like gas guzzlers will just drive those tweaked vehicles. But if instead there's just a carbon tax on fuel it's a lot harder to game your way around the legislative intent.

[1] Assuming that the balance between just paying the tax and evading the tax still favors paying it. You don't want to impose a $20/pack tax and find that you've just given organized crime a major boost.

That is indeed the point of the tax. For businesses all up and down the supply chain to figure out how to do what they do, but with less carbon production.

There's a whole lot of businesses where that's relatively easy, but since carbon is effectively free, they'll happily squander it for no real gain.