^Not so much the rural routes in Scotland, but think more about the high frequency routes. The rural routes can be quite busy throughout the year, providing often the only feasible public transport to these towns and villages. Even if they're not well used, it's often only a small number of trains that won't hugely affect the overall load factor.
However, in Greater Glasgow some of the trains throughout the day run with a very low load factor. Between 10am-2pm some routes continue to run at high frequency, and occasionally with long trains (where they can't split the train for whatever reason) but might have load factors in the single figures at times. Same in the evenings. With a high number of these services running not only in Glasgow but throughout the country, I suspect that it is these trains that will bring the overall load factor down.