There’s about 140,000 single passenger trips on the W Highland extenson each year. Whether that includes the Jacobite or not is unclear. Assuming not, that’s 400 people per day / 50 people per train on average through the year (that’s not 50 people end to end, albeit about 70% of them will be). Clearly they will be busier in the Easter - October period than the other half of the year.
The average revenue per passenger on Scotrail servcies on the line will be (educated guess) about £6, ie total revenue of about £900k. The marginal operating cost just for the train operator will be several multiples of that. It is clear that the busy trains in summer do not ‘pay for‘ the service in total, that’s a fact.
I offer no opinon on whether 400 people a day counts as lightly used or not, nor whether the costs being several multiples of income make it a basket case. It is a beautiful line, though, and does bring in some tourists (although not many, as the numbers show) and offers a service to locals. Albeit I suspect many locals who don‘t have access to a car will use the cheaper and quicker parallel bus service.