The taxes are not to encourage people not to use them. They're to make sure that the full cost of the flight is paid by the people taking the flight, rather than them just freeloading because the externalities are unaccounted for.
If that happens to discourage people from flying, well, that's just a side effect of having a properly functioning marketplace, where there are no externalities and the participants all have full information.
If that happens to discourage people from flying, well, that's just a side effect of having a properly functioning marketplace, where there are no externalities and the participants all have full information.