Why can't Jim get a better coffee/breakfast?

Because food is limited. They expect the crew to be awake for a month more than the passengers who are supposed to be awake a month prior to landfall. Unlike services like a phone call, food is budgeted ahead of time. At worst, Jim would have had one month of bad coffee before they landed, so it's expected he would suck it up. Instead he's going on a year and a few months. Food takes up space and is perishable, they wouldn't bring more than needed. And if they had brought extras for sale, there is no guarantee that it would be bought and would go to waste. That cuts into profits more than it would bring in revenue. It's a simple cost benefit analysis. Homestead is a capitalist venture after all.

Additionally, Jim is basically an indentured servant. He is paying for passage with his skills and labor. He's riding in credit as is. Unlike Aurora that paid full price. He has no money to buy with.

Practically speaking, he probably could upgrade, had a crew member been around. The company likely would allow upgrades, at a cost, if an employee could confirm that supplies arn't low and would override the system. Just like they did with Mac's employee ID and the AutoDoc.

Think of the spaceship like a cruise liner. All or most passengers will likely have three meals a day included in their tickets. I imagine Homestead don't really need passengers dying of starvation, so everyone gets fed and watered, except some get fed better than others.

If you skip to around 14m30s into the film when Jim is bashing away at the coffee machine, there the following exchange between the Jim and the machine:

Jim: "I want the mocha cappuccino extreme, bill my room please".

Machine: "Food can be purchased in the ship's...".

This suggests there's somewhere else on the ship where you can pay for better food or luxuries that aren't included in the cost of the ticket. In fact, later in the film, at around 40m:30s, when Jim meets Aurora for his "date", the following exchange takes place when Aurora admires Jim's sartorial upgrade:

Aurora: "You went shopping"

Jim: "I went shop lifting"

This suggests there are on-board shops, and Jim broke into one of them to obtain his suit. This would lead us to believe that if you have enough credit you can buy what you need, including better foods.