You should plan things for each system. If they stay aboard, refuel off a gas giant, etc., there are still possibilities of things happening. Other ships in the system, military or customs taking an interest in them etc.
Since most forms of Traveller require the ship receive periodic maintenance they should have to land at some point. The same goes for food, etc. There isn't an endless supply aboard.....
So now you have passengers and cargo (if it is a merchant), landing on worlds and going ashore (so to speak). This can and should lead to all sorts of possible things happening. Animal encounters, partron encounters, running into who-knows-what.
In fact, done well this sort of semi-random thing in each system.... carefully based on the UPP of the main world, and a good system description of the rest of it if necessary, you can come up with all sorts of things going on to keep the party interested. If the final destination is some sort of manditory option where the party has to eventually go there because they are left with little choice then eventually.... hopefully if they don't do stupid stuff and get killed off.... they will get there. But the trip should be interesting too.
Make each system interesting too. What would the world in each system be like? You can determine that before you start the game. Is world A a mining one while world B a resort? What goes on there? Why is the system like it is? How would the system end up with the UPP it has? If you know what the system is like then you have a starting point for events that occur there.
Taking some of the above:
You have a system with a dictator and high law level. The players plan on just jumping in, refueling, and jumping out..... Right up until the gas giant they are headed to 12 to 18 hours away (that's the typical range of transit times give or take) having a number of satellites one of which is a minor naval base of the system and the small warship(s) in orbit tell you to haul to and halt for an inspection and "refueling fee" because the local dictator makes alot of cash that way and demands twice or triple the usual unrefined fuel cost.....
Refueling itself will take 12+ hours depending on the size of the vessel and then another 12 to 18 out to the jump point.
Okay, the players have made 3 jumps and you tell them the next system they either land or start eating their shoes as the food has all but run out.... Problem is that system is nearly in starvation itself..... New problem for them to solve.
The idea here is to make them plan ahead and add detail to the game too. Don't just let them leave everything up to you....