No matter high /low capacity, airline can generate income if the plane is on the sky with sufficient passengers. That means airlines will utilise the aircrafts by maximising their operating hours.
Between long-haul flight(s) operated by large aircrafts, there may be some "gap" times, airline will operate some short-haul flight by the large aircarfts to fully utilise them.
Using China Southern as example, two of their a380s(B-6136 & B-6137) are used for short route CAN-BEK (~1100 miles) and at night they will be used for CAN-LAX (~7200 miles) and come back to Baiyun airport in the early morning of two days after (China time zone). However most of the other airlines has more complex schedules, the aircrafts used for EK857/858(DXB-KWI), the A380 shortest route(~550 miles), are used for many meduim/long-haul destinations, including MUM, JFK, HKG, LHR, SYD, BKK, FCO, BNE......
PS:Jon Story answer claimed that "long haul routes tend to have less frequent service with larger, higher capacity aircraft";however some airlines actually uses smaller aircrafts with more frequent services. Cathay have 5+ daily HKG-LHR routes (~6000miles) with b77W, exclude the night time there is approximately 3-4hrs average for each departures. Using "smaller" B777 (instead of A380) means more flexible choices for customers and the aircrafts can also be used for lower capacity long-haul routes.