Just from my standpoint (viewpoint if you will), the job of the GM/Referee is to try to create an atmosphere of "reality". A TV or Movie director will have some of his crew create/craft the seeming of an old Western Town by either:
A) Building a real town using real material, on real land, etc
or
B) Create what looks like the real thing with false fronts of buildings and making certain that the camera angle never shows the false front as anything but false.
Likewise, when a player, in charge of an imaginary starship, with imaginary crew, feeling imaginary hunger and fatigue, sets foot on imaginary alien soil (well, you get my drift) - tries to do something that is human in nature, but seem to be in response to the "realism" being crafted by the Referee for his sake.
So, why is there a distinction between rolling once for passengers versus Daily? Simple matter actually. In the span of 5 days, having X passengers and Y freight, and Z cargo, matters to a degree. Being limited to a finite number of resources in game play, will drive decision making on the part of the player. So, as a player, which would you rather have - five "flux" rolls giving you five times the number of high passage seeking passengers, or would you want to be limited to only one roll and perhaps not get your entire passenger manifest list with nothing but High Passage passengers?
Now, what if you as the Captain, had to say "yea or nay" to which passengers you'd permit on your craft, assuming that you have 4 staterooms and 6 potential passengers who all want space on the ship? Wouldn't you want to know something about them? What if after all four rooms were booked, two young newly-weds arrived with a young child in need of medical attention that can only be obtained off-world? And before you ask, she obviously had a child in the oven before the wedding was expected to take place...
Drama exists in many forms. For one campaign I ran, the player was the owner of his ship, and the longshoremen were trying to coerce the captain into paying for their services. "It would be a shame if something bad happened while loading your freight mister!" Instead, he refused their services. Next thing he knew, his steward/purser got waylaid in a bar one night, and every bone in the Purser's hand was broke and some serious damage done to the poor guy's body. The Captain had to choose between hiring a replacement purser for the job, or staying planetside and losing money. I never got to spring the Trap (campaign came to a halt), but the Steward being hired? He was in on the plot to hijack the ship. Ain't nothing like a hot cup of coffee right? Laced with sedatives? If the Purser is tasked with selecting which passengers get a berth on the ship, it isn't all too hard for a shady Purser to help take the ship and move on in life...
So - yes, the rules matter. If the GM doesn't like the rules, he of course can change them. That's what is happening with me right now in fact - I don't like the economics engine rules of GURPS FAR TRADER so I'm looking to something else to simulate how often certain freight lots will fill a given known sized ship, as well as how often passengers are available, etc. I don't want it to be so impossible to make a living by speculation that players pay off a 40 year loan in 1 year! Nor do I want it to be next to impossible that any speculation that is done is almost guaranteed to result in a loss of income!
<sigh>