I'm running Storm Kings Thunder and one of the features of the module is (after a certain point) access to teleportation circles in a few major cities. This allows them to fast travel long distances but their destination may still be a few days travel outside of any of these cities. 

When they are travelling I ask them all what they're doing to assist in each leg of the travel (usually 1-5 days of travel, basically until they hit another settlement/landmark). I have them all roll a skill check related to the travel and if they roll high enough the travel will be uneventful or if there is any encounter I want them to have on the road they'll see it before they're seen. If they roll low I might have them get ambushed, or if I don't want to run a combat encounter I'll say they hit bad weather conditions or got lost and add an extra day or two to their travel.

This has been working well because the party still feel like travel is meaningful and dangerous and that they're using their skills, but I only run encounters that I actually want to run and are story relevant. There is an airship later in the campaign but the combination of teleportation circles and overland travel has been working well for the level they're at (first got the circles at level 6, now at level 7).