I've never rented a car in Europe so have no sense of what you could a complish with a car on your day in Flam. The first thing I'd do is check the hours of the local rental car agency/agencies and try to figure out how early you can expect to get off the ship. How many hours' use would you get out of a one-day rental?
Then I'd consider the activities available to you without a car. There are two that are considered among Norway's very best experiences: the Flamsbana train up to Myrdal (1 hour; NOK 450 per person one-way--but you'd probably need a round-trip ticket, and I don't know how much that costs) and a trip into the Naeroyfjord by either ferry (NOK 570) or a more-expensive high-speed boat (2 hours). The fast boat (RIB) is a round trip. The ferry drops you off in Gudvangen, from which you'd either take the boat back or get the much faster shuttle bus (3/day; NOK 115, obviously also much cheaper than returning by boat).
I'm assuming your cruise doesn't go into the Naeroyfjord itself; if it goes all the way in, close to Gudvangen, you will already have that covered. Or maybe you'll feel as if you're seeing plenty of scenery from water level and don't mind missing the Naeroyfjord, even though it's considered the best in the area and one of the top two in the country.
As for what you can do with a car:
Drive up to the Stegastein viewpoint beyond Aurland. Said to be one of the best above-fjord viewpoints in the country. However, there are a few bus trips there each day, so you could do this without a car. Note: I don't know how well the departure times of those bus tours mesh with a round trip on the Flamsbana and/or the Naeroyfjord sightseeing trips by boat.
Drive over to the Borgund stave church, also beyond Aurland but on a different road. This, too, can theoretically be accomplished by public transportation. During peak season there's a daily (but I don't know about Saturday and Sunday) public Nor-Way bus departing Flam at noon. It allows about 1 hour at the church (unless the outbound bus is late, which mine was) before you have to catch the bus that gets you back to Flam just after 3 PM). That direct bus link may not be operating in September, and the best you might find would be a bus-bus-(long) walk routing, which is what was available back in the spring. That combination was going to take a lot longer than the 3-hour direct bus round trip, and I think many would consider it too time-consuming, not to mention risky, during a cruise stop.
If you want to see both the stave church and the Stegastein viewpoint, a car would probably be the most practical solution. The two should be easy to combine in far less than a day with a rental car at your disposal. But I don't know that you'd have time to fit in either the Flamsbana or a boat trip into the Naeroyfjord as well. All of the activities I've mentioned operate just a few times per day--and perhaps less often in September.
- Spending the full day in the car would allow you to go to Balestrand, perhaps farther.
Important: There is no longer a tourist information office in Flam. There is a large office with many people happy to sell you tickets for tours. I assume they provide accurate information on the departure times of the Flamsbana train, the boat trips into the Naeroyfjord (though not the cheaper Lustrabaatane boats to Gudvangen), the bus tours to the Stegastein viewpoint, etc. Those folks are not in the business of providing information about public bus service or other activities on which they cannot make money by getting commissions on ticket sales. If you are lucky, they will just tell you they cannot answer your questions. If you are not lucky, you may run into someone who (perhaps intentionally) gives you incorrect information. I was told there was no bus to the Borgund stave church. (Yes, I complained about that. A lot.)