So after reading a bit more (including your clarifications over on the Facebook thread), I understand what you're asking a bit more.
If I understand correctly, it's not "how do I solve this problem for this one adventure" as much as it's a more general "how do you make an air/raft a viable option in Traveller games without sacrificing all of your ground-based fun." Right?
Carrots
I know you would rather use the carrot than the stick. So what are the carrots?
If players spend all their time air/rafting around, just make the planet boring. They can go from settlement to settlement, but nothing really happens there. Especially on worlds with constant cloud cover or vegetation cover, they might not be able to really see what's happening on a planet from the air.
They can notice ground-based problems from the air. There's a fire in this spot and smoke rises. There's a distress call on a radio. There's a weird magnetic anomaly in this spot. The goal is to get them to land and explore.
You can't really talk to people from your air/raft. Make them land if they want to communicate with the natives. Give them reasons to ask people stuff.
They can't really explore or search from the air/raft. Make them land if they want to search caves, houses, crash sites, tight ravines, or underwater.
Put more adventures in the air! Large platforms, tall cliffs, laccolith towers, treetop villages, and so on--all will make the players glad they brought an air/raft.
Sticks
On the stick side (and I suspect people have mentioned this), air/rafts are usually open-top (routine vacc suit checks required for descent from orbit) and are very susceptible to weather (wind / lightning).
That means that if there's a highport but no downport, the local planet might want to control means of descent for various reasons: security, monopoly, unions, environmental protection, safety.
Consider the portmaster in certain islands today. A big ship comes in and wants to dock, and the portmaster takes over the ship for the last leg. The thought is, if the ship crashes into anything important, this small island's economy could be devastated for years while they rebuild their facilities. Roatan Island in the Caribbean has a large barrier reef, so large ships can't dock at all; they have to tender in (on large hovercraft!).
A planet might want to protect wildlife (weird flying jellyfish!) in a certain area of the planet, so they forbid any air traffic in large zones across the planet. If the PCs need to get there, they have to go on foot or maybe get a permit to take an EPA-approved ground vehicle.
There might be dangerous flying wildlife in an area, too, so while air/rafting might not be illegal, it's certainly discouraged. A laser rifle isn't going to be enough to protect them in their open-top gravitic flyer; and everyone on the planet knows that grynoks love attaching their suckers to gravitic drives and draining their power. Can't do that on every planet, obviously.