It actually depends on exactly what you're asking. Or even what you SHOULD be asking.
If you want the average profitability of all the 500+ operators in the Permian, you could just average all the profit margin percentages. This is taking the ratios (profit/revenue) for each company and averaging them. It corresponds to your expected (mean) profit margin if you just picked an operator at random.
If instead, I take all the profits and divide by all the revenues, this would give me the average profitability of the INDUSTRY (operators in the Permian). Often this is actually the question you are asking, or should be asking. IOW, you want the revenue-weighted average profit margin.
The same point would apply if you were, say doing sampling of different size demographic categories and were interested in the total population polling estimate. You need to weight by size of the buckets. (Or just take the totals, which is mathematically equivalent.)
Since we don't know exactly what you asked, or how precise you were, it's hard to say if the students were wrong. Of course, they may have been. But I would just check.
Responding to your edited-in update on the question. There's actually still some ambiguity about what you are (or should be) asking. But if I had to guess, the student's way is more likely giving the desired answer. (IOW, ratio the totals, rather than average the ratios.) IOW, "average fuel efficiency" should be "gallon" weighted. That's the one impacting your pocketbook.
In addition, you may find that there's some correlation of fuel efficiency with trip length. The engine being warmed up, operates more efficiently. Also, highway speeds may be more efficient than slow speeds. Also the issue of frequent stops and starts.
So if I were selecting a car, I would want the one that has the better average fuel efficiency (total miles/total gallons). Ideally with something approximating my type of usage. But I definitely wouldn't want to skew things by saying one "10 mile, 1 gallon" trip mean the same as one "100 mile, 5 gallon" trip in terms of the importance to my pocketbook.