Yes, the huge taxes are generally for international flights, and I think part of the reason is that, as you say, there aren't a lot of options for those flights so they have a captive market and are thus better able to bear those taxes. If you start with punitive taxes on domestic flights in the EU, it will disproportionately hit the airline industry there.

As with many things, the game with taxes is how to make the incidence of the tax fall more on the consumer and less on the producer. If you can accomplish that, then the tax is more likely to get through because unfortunately we don't have consumer lobbyists anywhere as strong as the business lobbyists.