It makes sense in a few ways. On a long high volume route sometimes you can't get as many frequencies as you would like out of one aircraft. So, since you can't do 2 or 3 frequencies with one aircraft, you go with one each from 2 or 3, or 2 with one and one from another, etc.
Also, say you are hubbed at LGA. Even if you're only running a few aircraft, it seems like many end up with an hour or 2 left once you're done scheduling them. Using more than one aircraft at the same price for one frequency each on a high volume short distance route like LGA-BOS, or LGA-PHL, is an easy way to maximize your fleet utilization and use those "scrap hours."